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<h3 style="margin-top: 20px; margin-bottom: 10px;">
Étienne Mollier pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/bbmap" style="color: #1068bf; text-decoration: none;">Debian Med / bbmap</a>
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<h4 style="margin-top: 10px; margin-bottom: 10px;">
Commits:
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<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/bbmap/-/commit/1c662261847da712e5b04b94277f8aa712c37619" style="color: #1068bf; text-decoration: none;">1c662261</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2022-08-03T13:38:44+02:00</i>
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<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: #fafafa; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dbdbdb;'>New upstream version 38.97+dfsg</pre>
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<h4 style="margin-top: 10px; margin-bottom: 10px;">30 changed files:</h4>
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<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d" style="color: #1068bf; text-decoration: none;">
README.md
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<a href="#35eed5db6f93b378bad3ac23d1eb656c1424333a" style="color: #1068bf; text-decoration: none;">
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Xcalcmem.sh
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<a href="#67d907d61087ac2bc1410f5791ecd5d94426cc74" style="color: #1068bf; text-decoration: none;">
bbduk.sh
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<a href="#4a18c3c5eec989524e435c6521f755ab31034d3a" style="color: #1068bf; text-decoration: none;">
clumpify.sh
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<a href="#49d09016d8268b25585bb4814ca03a279573d937" style="color: #1068bf; text-decoration: none;">
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current/clump/Hasher.java
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<a href="#5679e4c772d1c2b111dbcd93c6cd1d5a7c0f50e3" style="color: #1068bf; text-decoration: none;">
current/clump/KmerSort.java
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<a href="#090a5d3d3431125b6dff5f89cd4cc81c50dd2910" style="color: #1068bf; text-decoration: none;">
current/clump/KmerSort1.java
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<a href="#8abfd720134cdc771f6feb3c373cc6abe51c0f3d" style="color: #1068bf; text-decoration: none;">
current/clump/KmerSort2.java
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<a href="#c1f88416f8a24c20df9aefa087b5736241e082fa" style="color: #1068bf; text-decoration: none;">
current/clump/KmerSort3.java
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<a href="#8b67bed9478adfa01af5effee08f3ea398d80963" style="color: #1068bf; text-decoration: none;">
current/clump/KmerSplit.java
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<a href="#87e09ce245832e04b8a3d06edd667cfac9295e33" style="color: #1068bf; text-decoration: none;">
current/icecream/IceCreamFinder.java
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<a href="#06a7eaaf098b8d2e7c18a48b5d98671b027f6af9" style="color: #1068bf; text-decoration: none;">
current/jgi/BBDuk.java
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<a href="#635fa9bb7034f5bd7a766f17d0d6cc9b0800f06f" style="color: #1068bf; text-decoration: none;">
current/jgi/RQCFilter2.java
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<a href="#c1eb3ba3e50eb26c73088b4da40ccd2361d064a3" style="color: #1068bf; text-decoration: none;">
current/jgi/RQCFilterStats.java
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<a href="#187cd9d49b7c25c10731650b44504aafb9eb2fa1" style="color: #1068bf; text-decoration: none;">
current/shared/Parser.java
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<a href="#ef3b3e694c0bbaa70bf4c35a23c328ce44020fb6" style="color: #1068bf; text-decoration: none;">
current/shared/Shared.java
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<a href="#14fe639b07fd847461a2af0e6f8941d849848429" style="color: #1068bf; text-decoration: none;">
current/stream/FASTQ.java
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<a href="#a7cccac0c9e3ce8fcea270125d8329c409c781d1" style="color: #1068bf; text-decoration: none;">
current/tax/GiToTaxid.java
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<a href="#901bdbfa60205c675be60d3fa183dbbff4f5658b" style="color: #1068bf; text-decoration: none;">
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current/tax/GiToTaxidInt.java
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<a href="#ef479b2702704ccabfeb99dfbba06448b794752b" style="color: #1068bf; text-decoration: none;">
current/tax/TaxServer.java
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<a href="#f983ca3b863aeefdc8a5af4feffca4582a7fa91d" style="color: #1068bf; text-decoration: none;">
current/tax/TaxTree.java
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<a href="#2f1f31317e182ac33d5588ced7cd3e1807d82495" style="color: #1068bf; text-decoration: none;">
docs/changelog.txt
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<a href="#9987ab0d56f16295f54349f6c81020fd130981e3" style="color: #1068bf; text-decoration: none;">
removecatdogmousehuman.sh
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<a href="#20e87219ac67aaa797f562324d1b104fc07b648f" style="color: #1068bf; text-decoration: none;">
removehuman.sh
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<a href="#e3098a112479d051ffa11669086944ad085232cc" style="color: #1068bf; text-decoration: none;">
removehuman2.sh
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<a href="#098de73a43baa620dfd2d5bb4286132e821889eb" style="color: #1068bf; text-decoration: none;">
removemicrobes.sh
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<a href="#9f02f5242e6cef7d067a60833b9dcfe6d3692130" style="color: #1068bf; text-decoration: none;">
<span class="new-file">
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resources/PacBioAdapter.fa
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<a href="#3ceb66414e797c3aca775bd3535848b5bbdc22ba" style="color: #1068bf; text-decoration: none;">
resources/contents.txt
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<a href="#a7f35246a8c5f9ecfdce1ab90e6593332cb29506" style="color: #1068bf; text-decoration: none;">
resources/short.fa
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<a href="#1465556c39c436e4247078a91cfda5084218249e" style="color: #1068bf; text-decoration: none;">
shred.sh
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<h4 style="margin-top: 10px; margin-bottom: 10px;">Changes:</h4>
<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/bbmap/-/commit/1c662261847da712e5b04b94277f8aa712c37619#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d" style="color: #1068bf; text-decoration: none;"><strong style="font-weight: bold;">README.md</strong></a>
<hr style="overflow: hidden; border: 1px solid #e1e1e1;">
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -3,4 +3,4 @@</td>
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3
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<td class="new_line diff-line-num" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC3" class="line" lang="markdown"><span class="gh" style="color: #800080; font-weight: 600;"># Language: Java, Bash</span></span>
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<td class="old_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
4
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<td class="new_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
4
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC4" class="line" lang="markdown"><span class="gh" style="color: #800080; font-weight: 600;"># Information about documentation is in /docs/readme.txt.</span></span>
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<td class="old_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
5
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<td class="new_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
5
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC5" class="line" lang="markdown"></span>
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<td class="old_line diff-line-num old" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
6
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<td class="new_line diff-line-num old" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC6" class="line" lang="markdown"><span class="gh" style="color: #800080; font-weight: 600;"># Version 38.9<span class="idiff left right deletion" style="background-color: #fac5cd;">6</span></span></span></pre></td>
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<td class="old_line diff-line-num new" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
6
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC6" class="line" lang="markdown"><span class="gh" style="color: #800080; font-weight: 600;"># Version 38.9<span class="idiff left right addition" style="background-color: #c7f0d2;">7</span></span></span></pre></td>
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<br>
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<li id="35eed5db6f93b378bad3ac23d1eb656c1424333a">
<a href="https://salsa.debian.org/med-team/bbmap/-/commit/1c662261847da712e5b04b94277f8aa712c37619#35eed5db6f93b378bad3ac23d1eb656c1424333a" style="color: #1068bf; text-decoration: none;"><strong style="font-weight: bold;">Xcalcmem.sh</strong></a>
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<td class="new_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash</span></span>
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2
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC2" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#calcmem</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3" class="line" lang="shell"></span>
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<td class="new_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
4
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC4" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#function usage(){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
5
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC5" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># echo "CalcMem v1.01"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
6
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC6" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># echo "Written by Brian Bushnell, Doug Jacobsen, Alex Copeland"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
7
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC7" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># echo "Calculates available memory in megabytes"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
8
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC8" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># echo "Last modified April 25, 2014"</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
9
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC9" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
10
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC10" class="line" lang="shell"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
11
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC11" class="line" lang="shell"><span class="k" style="font-weight: 600;">function </span>parseXmx <span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
12
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC12" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">local </span><span class="nv" style="color: #008080;">setxmx</span><span class="o" style="font-weight: 600;">=</span>0</span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
13
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC13" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">local </span><span class="nv" style="color: #008080;">setxms</span><span class="o" style="font-weight: 600;">=</span>0</span>
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<td class="new_line diff-line-num new" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
14
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC14" class="line" lang="shell"> </span>
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<td class="new_line diff-line-num new" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
15
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC15" class="line" lang="shell"> <span class="k" style="font-weight: 600;">for </span>arg <span class="k" style="font-weight: 600;">in</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$@</span><span class="s2" style="color: #d14;">"</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
16
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC16" class="line" lang="shell"> <span class="k" style="font-weight: 600;">do</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
17
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC17" class="line" lang="shell"><span class="k" style="font-weight: 600;"> if</span> <span class="o" style="font-weight: 600;">[[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$arg</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">==</span> <span class="nt" style="color: #000080;">-Xmx</span><span class="k" style="font-weight: 600;">*</span> <span class="o" style="font-weight: 600;">]]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<td class="new_line diff-line-num new" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
18
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC18" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">z</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$arg</span><span class="s2" style="color: #d14;">"</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
19
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC19" class="line" lang="shell"> <span class="nv" style="color: #008080;">setxmx</span><span class="o" style="font-weight: 600;">=</span>1</span>
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<td class="new_line diff-line-num new" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
20
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC20" class="line" lang="shell"> <span class="k" style="font-weight: 600;">elif</span> <span class="o" style="font-weight: 600;">[[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$arg</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">==</span> Xmx<span class="k" style="font-weight: 600;">*</span> <span class="o" style="font-weight: 600;">]]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<td class="new_line diff-line-num new" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
21
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC21" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">z</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"-</span><span class="nv" style="color: #008080;">$arg</span><span class="s2" style="color: #d14;">"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
22
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC22" class="line" lang="shell"> <span class="nv" style="color: #008080;">setxmx</span><span class="o" style="font-weight: 600;">=</span>1</span>
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23
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC23" class="line" lang="shell"> <span class="k" style="font-weight: 600;">elif</span> <span class="o" style="font-weight: 600;">[[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$arg</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">==</span> <span class="nt" style="color: #000080;">-Xms</span><span class="k" style="font-weight: 600;">*</span> <span class="o" style="font-weight: 600;">]]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<td class="new_line diff-line-num new" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
24
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC24" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">z2</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$arg</span><span class="s2" style="color: #d14;">"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
25
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC25" class="line" lang="shell"> <span class="nv" style="color: #008080;">setxms</span><span class="o" style="font-weight: 600;">=</span>1</span>
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<td class="new_line diff-line-num new" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
26
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC26" class="line" lang="shell"> <span class="k" style="font-weight: 600;">elif</span> <span class="o" style="font-weight: 600;">[[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$arg</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">==</span> Xms<span class="k" style="font-weight: 600;">*</span> <span class="o" style="font-weight: 600;">]]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<td class="new_line diff-line-num new" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
27
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC27" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">z2</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"-</span><span class="nv" style="color: #008080;">$arg</span><span class="s2" style="color: #d14;">"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
28
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC28" class="line" lang="shell"> <span class="nv" style="color: #008080;">setxms</span><span class="o" style="font-weight: 600;">=</span>1</span>
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<td class="new_line diff-line-num new" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
29
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC29" class="line" lang="shell"> <span class="k" style="font-weight: 600;">elif</span> <span class="o" style="font-weight: 600;">[[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$arg</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">==</span> <span class="nt" style="color: #000080;">-da</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="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$arg</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">==</span> <span class="nt" style="color: #000080;">-ea</span> <span class="o" style="font-weight: 600;">]]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<td class="new_line diff-line-num new" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
30
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC30" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">EA</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$arg</span><span class="s2" style="color: #d14;">"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
31
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC31" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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<td class="new_line diff-line-num new" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
32
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC32" class="line" lang="shell"><span class="k" style="font-weight: 600;"> done</span></span>
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<td class="new_line diff-line-num new" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
33
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC33" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span></span>
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<td class="new_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
34
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC34" class="line" lang="shell"><span class="k" style="font-weight: 600;"> if</span> <span class="o" style="font-weight: 600;">[[</span> <span class="nv" style="color: #008080;">$setxmx</span> <span class="o" style="font-weight: 600;">==</span> 1 <span class="o" style="font-weight: 600;">]]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">[[</span> <span class="nv" style="color: #008080;">$setxms</span> <span class="o" style="font-weight: 600;">==</span> 0 <span class="o" style="font-weight: 600;">]]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<td class="new_line diff-line-num new" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
35
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC35" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">local </span><span class="nv" style="color: #008080;">substring</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$z</span>| <span class="nb" style="color: #0086b3;">cut</span> <span class="nt" style="color: #000080;">-d</span><span class="s1" style="color: #d14;">'x'</span> <span class="nt" style="color: #000080;">-f</span> 2<span class="sb" style="color: #d14;">`</span></span>
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<td class="new_line diff-line-num new" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
36
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC36" class="line" lang="shell"> <span class="nv" style="color: #008080;">z2</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"-Xms</span><span class="nv" style="color: #008080;">$substring</span><span class="s2" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
37
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC37" class="line" lang="shell"> <span class="nv" style="color: #008080;">setxms</span><span class="o" style="font-weight: 600;">=</span>1</span>
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<td class="new_line diff-line-num new" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
38
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC38" class="line" lang="shell"> <span class="k" style="font-weight: 600;">elif</span> <span class="o" style="font-weight: 600;">[[</span> <span class="nv" style="color: #008080;">$setxmx</span> <span class="o" style="font-weight: 600;">==</span> 0 <span class="o" style="font-weight: 600;">]]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">[[</span> <span class="nv" style="color: #008080;">$setxms</span> <span class="o" style="font-weight: 600;">==</span> 1 <span class="o" style="font-weight: 600;">]]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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39
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC39" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">local </span><span class="nv" style="color: #008080;">substring</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$z2</span>| <span class="nb" style="color: #0086b3;">cut</span> <span class="nt" style="color: #000080;">-d</span><span class="s1" style="color: #d14;">'s'</span> <span class="nt" style="color: #000080;">-f</span> 2<span class="sb" style="color: #d14;">`</span></span>
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<td class="new_line diff-line-num new" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
40
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC40" class="line" lang="shell"> <span class="nv" style="color: #008080;">z</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"-Xmx</span><span class="nv" style="color: #008080;">$substring</span><span class="s2" style="color: #d14;">"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
41
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC41" class="line" lang="shell"> <span class="nv" style="color: #008080;">setxmx</span><span class="o" style="font-weight: 600;">=</span>1</span>
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<td class="new_line diff-line-num new" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
42
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC42" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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<td class="new_line diff-line-num new" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
43
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC43" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span></span>
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<td class="new_line diff-line-num new" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
44
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC44" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">set</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$setxmx</span></span>
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45
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC45" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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46
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC46" class="line" lang="shell"></span>
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<td class="new_line diff-line-num new" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
47
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC47" class="line" lang="shell"></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
48
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC48" class="line" lang="shell"><span class="nv" style="color: #008080;">RAM</span><span class="o" style="font-weight: 600;">=</span>0<span class="p">;</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
49
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC49" class="line" lang="shell"></span>
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<td class="new_line diff-line-num new" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
50
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC50" class="line" lang="shell"><span class="k" style="font-weight: 600;">function </span>freeRam<span class="o" style="font-weight: 600;">(){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
51
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC51" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">#Memory is in kilobytes.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
52
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC52" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">local </span><span class="nv" style="color: #008080;">defaultMem</span><span class="o" style="font-weight: 600;">=</span>3200000</span>
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<td class="new_line diff-line-num new" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
53
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC53" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$# </span><span class="nt" style="color: #000080;">-gt</span> 0 <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<td class="new_line diff-line-num new" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
54
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC54" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">defaultMem</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$1</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
55
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC55" class="line" lang="shell"> <span class="k" style="font-weight: 600;">case</span> <span class="nv" style="color: #008080;">$defaultMem</span> <span class="k" style="font-weight: 600;">in</span></span>
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<td class="new_line diff-line-num new" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
56
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC56" class="line" lang="shell"> <span class="k" style="font-weight: 600;">*</span>g<span class="p">)</span></span>
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57
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC57" class="line" lang="shell"> <span class="nv" style="color: #008080;">defaultMem</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$defaultMem</span>| <span class="nb" style="color: #0086b3;">cut</span> <span class="nt" style="color: #000080;">-d</span><span class="s1" style="color: #d14;">'g'</span> <span class="nt" style="color: #000080;">-f</span> 1<span class="sb" style="color: #d14;">`</span></span>
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<td class="new_line diff-line-num new" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
58
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC58" class="line" lang="shell"> <span class="nv" style="color: #008080;">defaultMem</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">$((</span> <span class="nv" style="color: #008080;">$defaultMem</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">$((</span> <span class="m" style="color: #099;">1024</span> <span class="o" style="font-weight: 600;">*</span> <span class="m" style="color: #099;">1024</span> <span class="k" style="font-weight: 600;">))</span> <span class="k" style="font-weight: 600;">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
59
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC59" class="line" lang="shell"> <span class="p">;;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
60
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC60" class="line" lang="shell"> <span class="k" style="font-weight: 600;">*</span>m<span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
61
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC61" class="line" lang="shell"> <span class="nv" style="color: #008080;">defaultMem</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$defaultMem</span>| <span class="nb" style="color: #0086b3;">cut</span> <span class="nt" style="color: #000080;">-d</span><span class="s1" style="color: #d14;">'m'</span> <span class="nt" style="color: #000080;">-f</span> 1<span class="sb" style="color: #d14;">`</span></span>
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<td class="new_line diff-line-num new" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
62
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC62" class="line" lang="shell"> <span class="nv" style="color: #008080;">defaultMem</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">$((</span> <span class="nv" style="color: #008080;">$defaultMem</span> <span class="o" style="font-weight: 600;">*</span> <span class="m" style="color: #099;">1024</span> <span class="k" style="font-weight: 600;">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
63
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC63" class="line" lang="shell"> <span class="p">;;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
64
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC64" class="line" lang="shell"> <span class="k" style="font-weight: 600;">*</span>k<span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
65
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC65" class="line" lang="shell"> <span class="nv" style="color: #008080;">defaultMem</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$defaultMem</span>| <span class="nb" style="color: #0086b3;">cut</span> <span class="nt" style="color: #000080;">-d</span><span class="s1" style="color: #d14;">'k'</span> <span class="nt" style="color: #000080;">-f</span> 1<span class="sb" style="color: #d14;">`</span></span>
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<td class="new_line diff-line-num new" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
66
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC66" class="line" lang="shell"> <span class="p">;;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
67
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC67" class="line" lang="shell"> <span class="k" style="font-weight: 600;">esac</span></span>
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<td class="new_line diff-line-num new" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
68
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC68" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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<td class="new_line diff-line-num new" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
69
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC69" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span></span>
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<td class="new_line diff-line-num new" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
70
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC70" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">local </span><span class="nv" style="color: #008080;">mult</span><span class="o" style="font-weight: 600;">=</span>84</span>
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<td class="new_line diff-line-num new" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
71
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC71" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$# </span><span class="nt" style="color: #000080;">-gt</span> 1 <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<td class="new_line diff-line-num new" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
72
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC72" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">mult</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$2</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
73
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC73" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
74
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC74" class="line" lang="shell"> </span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
75
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC75" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">#echo "mult = $mult"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
76
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC76" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">#echo "default = $defaultMem"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
77
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC77" class="line" lang="shell"> </span>
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<td class="new_line diff-line-num new" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
78
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC78" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">local ulimit</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">ulimit</span> <span class="nt" style="color: #000080;">-v</span><span class="si" style="color: #d14;">)</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
79
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC79" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">local </span><span class="nv" style="color: #008080;">x</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$ulimit</span></span>
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<td class="new_line diff-line-num new" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
80
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC80" class="line" lang="shell"> </span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
81
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC81" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-e</span> /proc/meminfo <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<td class="new_line diff-line-num new" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
82
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC82" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">local </span><span class="nv" style="color: #008080;">vfree</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">cat</span> /proc/meminfo | <span class="nb" style="color: #0086b3;">awk</span> <span class="nt" style="color: #000080;">-F</span>: <span class="s1" style="color: #d14;">'BEGIN{total=-1;used=-1} /^CommitLimit:/ { total=$2 }; /^Committed_AS:/ { used=$2 } END{ print (total-used) }'</span><span class="si" style="color: #d14;">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
83
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC83" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">local </span><span class="nv" style="color: #008080;">pfree</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">cat</span> /proc/meminfo | <span class="nb" style="color: #0086b3;">awk</span> <span class="nt" style="color: #000080;">-F</span>: <span class="s1" style="color: #d14;">'BEGIN{free=-1;cached=-1;buffers=-1} /^MemFree:/ { free=$2 }; /^Cached:/ { cached=$2}; /^Buffers:/ { buffers=$2} END{ print (free+cached+buffers) }'</span><span class="si" style="color: #d14;">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
84
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC84" class="line" lang="shell"> </span>
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<td class="new_line diff-line-num new" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
85
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC85" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"vfree = </span><span class="nv" style="color: #008080;">$vfree</span><span class="s2" style="color: #d14;">"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
86
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC86" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"pfree = </span><span class="nv" style="color: #008080;">$pfree</span><span class="s2" style="color: #d14;">"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
87
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC87" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"ulimit = </span><span class="nv" style="color: #008080;">$ulimit</span><span class="s2" style="color: #d14;">"</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
88
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC88" class="line" lang="shell"></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
89
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC89" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">local </span><span class="nv" style="color: #008080;">x2</span><span class="o" style="font-weight: 600;">=</span>0<span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
90
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC90" class="line" lang="shell"> </span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
91
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC91" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$vfree</span> <span class="nt" style="color: #000080;">-gt</span> 0 <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$pfree</span> <span class="nt" style="color: #000080;">-gt</span> 0 <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
92
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC92" class="line" lang="shell"><span class="k" style="font-weight: 600;"> if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$vfree</span> <span class="nt" style="color: #000080;">-gt</span> <span class="nv" style="color: #008080;">$pfree</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nv" style="color: #008080;">x2</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$pfree</span><span class="p">;</span> </span>
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<td class="new_line diff-line-num new" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
93
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC93" class="line" lang="shell"> <span class="k" style="font-weight: 600;">else </span><span class="nv" style="color: #008080;">x2</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$vfree</span><span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span></span>
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<td class="new_line diff-line-num new" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
94
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC94" class="line" lang="shell"><span class="k" style="font-weight: 600;"> elif</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$vfree</span> <span class="nt" style="color: #000080;">-gt</span> 0 <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nv" style="color: #008080;">x2</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$vfree</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
95
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC95" class="line" lang="shell"> <span class="k" style="font-weight: 600;">elif</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$pfree</span> <span class="nt" style="color: #000080;">-gt</span> 0 <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nv" style="color: #008080;">x2</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$pfree</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
96
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC96" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
97
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC97" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
98
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC98" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$x</span></span>
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<td class="new_line diff-line-num new" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
99
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC99" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$x2</span></span>
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<td class="new_line diff-line-num new" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
100
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC100" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$vfree</span></span>
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<td class="new_line diff-line-num new" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
101
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC101" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$pfree</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
102
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC102" class="line" lang="shell"> </span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
103
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC103" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$x</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">"unlimited"</span> <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">((</span><span class="nv" style="color: #008080;">$x</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$x2</span><span class="o" style="font-weight: 600;">))</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nv" style="color: #008080;">x</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$x2</span><span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span></span>
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<td class="new_line diff-line-num new" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
104
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC104" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span></span>
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<td class="new_line diff-line-num new" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
105
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC105" class="line" lang="shell"><span class="k" style="font-weight: 600;"> fi</span></span>
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<td class="new_line diff-line-num new" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
106
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC106" class="line" lang="shell"> </span>
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<td class="new_line diff-line-num new" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
107
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC107" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">#echo "x=$x"</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
108
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC108" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">local </span><span class="nv" style="color: #008080;">HOSTNAME</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">hostname</span><span class="sb" style="color: #d14;">`</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
109
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC109" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$x</span> <span class="nt" style="color: #000080;">-lt</span> 1 <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="nv" style="color: #008080;">$HOSTNAME</span> <span class="o" style="font-weight: 600;">==</span> genepool<span class="k" style="font-weight: 600;">*</span> <span class="o" style="font-weight: 600;">]]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
110
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC110" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">#echo "hello 2"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
111
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC111" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">#echo $x</span></span>
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<td class="new_line diff-line-num new" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
112
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC112" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">#echo "ram is unlimited"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
113
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC113" class="line" lang="shell"> <span class="nv" style="color: #008080;">RAM</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">$((</span>defaultMem/1024<span class="k" style="font-weight: 600;">))</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
114
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC114" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Max memory cannot be determined. Attempting to use </span><span class="nv" style="color: #008080;">$RAM</span><span class="s2" style="color: #d14;"> MB."</span> 1>&2</span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
115
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC115" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"If this fails, please set ulimit or run this program qsubbed or from a qlogin session on Genepool."</span> 1>&2</span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
116
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC116" class="line" lang="shell"> <span class="k" style="font-weight: 600;">else</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
117
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC117" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">#echo "hello 1"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
118
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC118" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">#echo $x</span></span>
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<td class="new_line diff-line-num new" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
119
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC119" class="line" lang="shell"> </span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
120
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC120" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">#if [ $x -ge 1000000000 ]; then</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
121
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC121" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># echo "ram is 1000g+"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
122
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC122" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">#elif [ $x -ge 500000000 ]; then</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
123
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC123" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># echo "ram is 500g+"</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
124
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC124" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">#elif [ $x -ge 250000000 ]; then</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
125
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC125" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># echo "ram is 250g+"</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
126
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC126" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">#elif [ $x -ge 144000000 ]; then</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
127
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC127" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># echo "ram is 144g+"</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
128
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC128" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">#elif [ $x -ge 120000000 ]; then</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
129
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC129" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># echo "ram is 120g+"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
130
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC130" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">#elif [ $x -ge 40000000 ]; then</span></span>
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<td class="new_line diff-line-num new" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
131
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC131" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># echo "ram is 40g+"</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
132
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC132" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">#else</span></span>
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<td class="new_line diff-line-num new" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
133
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC133" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># echo "ram is under 40g"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
134
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC134" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">#fi</span></span>
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<td class="new_line diff-line-num new" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
135
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC135" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">#echo $x</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
136
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC136" class="line" lang="shell"> <span class="nv" style="color: #008080;">RAM</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">$((</span> <span class="o" style="font-weight: 600;">((</span>x-500000<span class="o" style="font-weight: 600;">)*</span>mult/100<span class="o" style="font-weight: 600;">)/</span><span class="m" style="color: #099;">1024</span> <span class="k" style="font-weight: 600;">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
137
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC137" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">#echo $RAM</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
138
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC138" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
139
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC139" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
140
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC140" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$set</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
141
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC141" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$z</span></span>
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<td class="new_line diff-line-num new" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
142
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC142" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$z2</span></span>
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<td class="new_line diff-line-num new" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
143
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC143" class="line" lang="shell"> </span>
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<td class="new_line diff-line-num new" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
144
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC144" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">#local z="-Xmx${RAM}m"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
145
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC145" class="line" lang="shell"> <span class="k" style="font-weight: 600;">return </span>0</span>
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<td class="new_line diff-line-num new" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
146
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148
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC148" class="line" lang="shell">parseXmx <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$@</span><span class="s2" style="color: #d14;">"</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
149
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC149" class="line" lang="shell">freeRam <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$@</span><span class="s2" style="color: #d14;">"</span></span></pre></td>
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<a href="https://salsa.debian.org/med-team/bbmap/-/commit/1c662261847da712e5b04b94277f8aa712c37619#67d907d61087ac2bc1410f5791ecd5d94426cc74" style="color: #1068bf; text-decoration: none;"><strong style="font-weight: bold;">bbduk.sh</strong></a>
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<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -3,7 +3,7 @@</td>
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<td class="old_line diff-line-num" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
3
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<td class="new_line diff-line-num" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
3
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC3" class="line" lang="shell">usage<span class="o" style="font-weight: 600;">(){</span></span>
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4
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<td class="new_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
4
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC4" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span></span>
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5
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<td class="new_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
5
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC5" class="line" lang="shell"><span class="s2" style="color: #d14;">Written by Brian Bushnell</span></span>
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<td class="old_line diff-line-num old" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
6
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<td class="new_line diff-line-num old" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC6" class="line" lang="shell"><span class="s2" style="color: #d14;">Last modified J<span class="idiff left deletion" style="background-color: #fac5cd;">anuar</span>y 2<span class="idiff deletion" style="background-color: #fac5cd;">6</span>, 202<span class="idiff right deletion" style="background-color: #fac5cd;">1</span></span></span>
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<td class="new_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
6
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC6" class="line" lang="shell"><span class="s2" style="color: #d14;">Last modified J<span class="idiff left addition" style="background-color: #c7f0d2;">ul</span>y 2<span class="idiff addition" style="background-color: #c7f0d2;">8</span>, 202<span class="idiff right addition" style="background-color: #c7f0d2;">2</span></span></span>
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7
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<td class="new_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
7
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC7" class="line" lang="shell"></span>
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<td class="old_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
8
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<td class="new_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
8
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC8" class="line" lang="shell"><span class="s2" style="color: #d14;">Description: Compares reads to the kmers in a reference dataset, optionally </span></span>
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<td class="old_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
9
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<td class="new_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
9
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC9" class="line" lang="shell"><span class="s2" style="color: #d14;">allowing an edit distance. Splits the reads into two outputs - those that </span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -172,11 +172,14 @@ Note - if ktrim, kmask, and ksplit are unset, the default behavior is kfilter.</td>
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<td class="old_line diff-line-num" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
172
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<td class="new_line diff-line-num" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
172
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC172" class="line" lang="shell"><span class="s2" style="color: #d14;">All kmer processing modes are mutually exclusive.</span></span>
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<td class="old_line diff-line-num" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
173
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<td class="new_line diff-line-num" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
173
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC173" class="line" lang="shell"><span class="s2" style="color: #d14;">Reads only get sent to 'outm' purely based on kmer matches in kfilter mode.</span></span>
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<td class="old_line diff-line-num" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
174
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<td class="new_line diff-line-num" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
174
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC174" class="line" lang="shell"></span>
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<td class="old_line diff-line-num old" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
175
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<td class="new_line diff-line-num old" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC175" class="line" lang="shell"><span class="s2" style="color: #d14;">ktrim=f Trim reads to remove bases matching reference kmers.</span></span>
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<td class="old_line diff-line-num new" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
175
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC175" class="line" lang="shell"><span class="s2" style="color: #d14;">ktrim=f Trim reads to remove bases matching reference kmers, plus</span></span>
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<td class="old_line diff-line-num new" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
176
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC176" class="line" lang="shell"><span class="s2" style="color: #d14;"> all bases to the left or right.</span></span>
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176
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177
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC177" class="line" lang="shell"><span class="s2" style="color: #d14;"> Values: </span></span>
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177
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<td class="new_line diff-line-num" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
178
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC178" class="line" lang="shell"><span class="s2" style="color: #d14;"> f (don't trim), </span></span>
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178
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<td class="new_line diff-line-num" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
179
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC179" class="line" lang="shell"><span class="s2" style="color: #d14;"> r (trim to the right), </span></span>
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179
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<td class="new_line diff-line-num" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
180
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC180" class="line" lang="shell"><span class="s2" style="color: #d14;"> l (trim to the left)</span></span>
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<td class="old_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
181
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC181" class="line" lang="shell"><span class="s2" style="color: #d14;">ktrimtips=0 Set this to a positive number to perform ktrim on both</span></span>
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<td class="new_line diff-line-num new" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
182
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC182" class="line" lang="shell"><span class="s2" style="color: #d14;"> ends, examining only the outermost X bases.</span></span>
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<td class="old_line diff-line-num" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
180
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<td class="new_line diff-line-num" 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: inherit;" align="right" bgcolor="#fafafa">
183
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC183" class="line" lang="shell"><span class="s2" style="color: #d14;">kmask= Replace bases matching ref kmers with another symbol.</span></span>
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181
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<td class="new_line diff-line-num" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
184
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC184" class="line" lang="shell"><span class="s2" style="color: #d14;"> Allows any non-whitespace character, and processes short</span></span>
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<td class="old_line diff-line-num" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
182
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<td class="new_line diff-line-num" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
185
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC185" class="line" lang="shell"><span class="s2" style="color: #d14;"> kmers on both ends if mink is set. 'kmask=lc' will</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -237,6 +240,8 @@ restrictleft=0 If positive, only look for kmer matches in the</td>
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237
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<td class="new_line diff-line-num" data-linenumber="240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
240
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC240" class="line" lang="shell"><span class="s2" style="color: #d14;"> leftmost X bases.</span></span>
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<td class="old_line diff-line-num" data-linenumber="238" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
238
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<td class="new_line diff-line-num" data-linenumber="241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
241
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC241" class="line" lang="shell"><span class="s2" style="color: #d14;">restrictright=0 If positive, only look for kmer matches in the </span></span>
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<td class="old_line diff-line-num" data-linenumber="239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
239
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<td class="new_line diff-line-num" data-linenumber="242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
242
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC242" class="line" lang="shell"><span class="s2" style="color: #d14;"> rightmost X bases.</span></span>
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<td class="old_line diff-line-num new" data-linenumber="240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
243
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC243" class="line" lang="shell"><span class="s2" style="color: #d14;">NOTE: restrictleft and restrictright are mutually exclusive. If trimming</span></span>
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<td class="old_line diff-line-num new" data-linenumber="240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
244
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC244" class="line" lang="shell"><span class="s2" style="color: #d14;"> both ends is desired, use ktrimtips.</span></span>
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<td class="old_line diff-line-num" data-linenumber="240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
240
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<td class="new_line diff-line-num" data-linenumber="245" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
245
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC245" class="line" lang="shell"><span class="s2" style="color: #d14;">mingc=0 Discard reads with GC content below this.</span></span>
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<td class="old_line diff-line-num" data-linenumber="241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
241
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<td class="new_line diff-line-num" data-linenumber="246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
246
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC246" class="line" lang="shell"><span class="s2" style="color: #d14;">maxgc=1 Discard reads with GC content above this.</span></span>
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<td class="old_line diff-line-num" data-linenumber="242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
242
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<td class="new_line diff-line-num" data-linenumber="247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
247
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC247" class="line" lang="shell"><span class="s2" style="color: #d14;">gcpairs=t Use average GC of paired reads.</span></span>
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<a href="https://salsa.debian.org/med-team/bbmap/-/commit/1c662261847da712e5b04b94277f8aa712c37619#4a18c3c5eec989524e435c6521f755ab31034d3a" style="color: #1068bf; text-decoration: none;"><strong style="font-weight: bold;">clumpify.sh</strong></a>
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<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -3,7 +3,7 @@</td>
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3
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3
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC3" class="line" lang="shell">usage<span class="o" style="font-weight: 600;">(){</span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC4" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC5" class="line" lang="shell"><span class="s2" style="color: #d14;">Written by Brian Bushnell</span></span>
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC6" class="line" lang="shell"><span class="s2" style="color: #d14;">Last modified <span class="idiff left deletion" style="background-color: #fac5cd;">October 30</span>, 20<span class="idiff right deletion" style="background-color: #fac5cd;">19</span></span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC6" class="line" lang="shell"><span class="s2" style="color: #d14;">Last modified <span class="idiff left addition" style="background-color: #c7f0d2;">July 28</span>, 20<span class="idiff right addition" style="background-color: #c7f0d2;">22</span></span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC7" class="line" lang="shell"></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC8" class="line" lang="shell"><span class="s2" style="color: #d14;">Description: Sorts sequences to put similar reads near each other.</span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC9" class="line" lang="shell"><span class="s2" style="color: #d14;">Can be used for increased compression or error correction.</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -95,6 +95,9 @@ allduplicates=f Mark or remove all copies of duplicates, instead of</td>
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<td class="old_line diff-line-num" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
95
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<td class="new_line diff-line-num" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
95
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC95" class="line" lang="shell"><span class="s2" style="color: #d14;"> keeping the highest-quality copy.</span></span>
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<td class="old_line diff-line-num" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
96
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<td class="new_line diff-line-num" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
96
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC96" class="line" lang="shell"><span class="s2" style="color: #d14;">addcount=f Append the number of copies to the read name.</span></span>
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<td class="old_line diff-line-num" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
97
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<td class="new_line diff-line-num" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
97
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC97" class="line" lang="shell"><span class="s2" style="color: #d14;"> Mutually exclusive with markduplicates or allduplicates.</span></span>
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<td class="old_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
98
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC98" class="line" lang="shell"><span class="s2" style="color: #d14;">entryfilter=f This assists in removing exact duplicates, which saves</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
99
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC99" class="line" lang="shell"><span class="s2" style="color: #d14;"> memory in libraries that split unevenly due to huge</span></span>
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<td class="old_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
100
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC100" class="line" lang="shell"><span class="s2" style="color: #d14;"> numbers of duplicates. Enabled automatically as needed.</span></span>
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<td class="old_line diff-line-num" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
98
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<td class="new_line diff-line-num" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
101
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC101" class="line" lang="shell"><span class="s2" style="color: #d14;">subs=2 (s) Maximum substitutions allowed between duplicates.</span></span>
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<td class="old_line diff-line-num" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
99
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<td class="new_line diff-line-num" 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: inherit;" align="right" bgcolor="#fafafa">
102
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC102" class="line" lang="shell"><span class="s2" style="color: #d14;">subrate=0.0 (dsr) If set, the number of substitutions allowed will be</span></span>
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100
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<td class="new_line diff-line-num" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
103
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC103" class="line" lang="shell"><span class="s2" style="color: #d14;"> max(subs, subrate*min(length1, length2)) for 2 sequences.</span></span>
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<a href="https://salsa.debian.org/med-team/bbmap/-/commit/1c662261847da712e5b04b94277f8aa712c37619#49d09016d8268b25585bb4814ca03a279573d937" style="color: #1068bf; text-decoration: none;"><strong style="font-weight: bold;">current/clump/Hasher.java</strong></a>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1" class="line" lang="java"><span class="kn" style="font-weight: 600;">package</span> <span class="nn" style="color: #555;">clump</span><span class="o" style="font-weight: 600;">;</span></span>
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3
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.Random</span><span class="o" style="font-weight: 600;">;</span></span>
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4
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC4" class="line" lang="java"></span>
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<td class="new_line diff-line-num new" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
5
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC5" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">shared.Tools</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
6
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC6" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">stream.Read</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
7
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC7" class="line" lang="java"></span>
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<td class="new_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
8
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC8" 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;">Hasher</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
9
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC9" class="line" lang="java"></span>
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<td class="new_line diff-line-num new" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
10
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC10" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">synchronized</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">[][]</span> <span class="nf" style="color: #900; font-weight: 600;">makeCodes2</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;">modes</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
11
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC11" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">[][]</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">makeCodes</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">128</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">modes</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
12
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC12" class="line" lang="java"> </span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
13
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC13" 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="mi" style="color: #099;">26</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
14
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC14" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">=(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">)(</span><span class="sc" style="color: #d14;">'A'</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
15
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC15" class="line" lang="java"> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">[</span><span class="nc" style="color: #458; font-weight: 600;">Tools</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="n" style="color: #333;">c</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;">c</span><span class="o" style="font-weight: 600;">];</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
16
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC16" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
17
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC17" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">;</span></span>
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18
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC18" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC19" class="line" lang="java"> </span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC20" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">synchronized</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">[][]</span> <span class="nf" style="color: #900; font-weight: 600;">makeCodes</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;">symbols</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;">modes</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
21
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC21" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Random</span> <span class="n" style="color: #333;">randy</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;">Random</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
22
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC22" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">[][]</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">symbols</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">modes</span><span class="o" style="font-weight: 600;">];</span></span>
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<td class="new_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
23
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC23" 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;">symbols</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
24
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC24" 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;">modes</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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<td class="new_line diff-line-num new" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
25
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC25" class="line" lang="java"> <span class="n" style="color: #333;">r</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;">j</span><span class="o" style="font-weight: 600;">]=</span><span class="n" style="color: #333;">randy</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextLong</span><span class="o" style="font-weight: 600;">();</span></span>
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<td class="new_line diff-line-num new" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
26
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC26" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
27
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC27" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
28
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC28" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">;</span></span>
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29
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC29" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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30
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC30" class="line" lang="java"> </span>
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<td class="new_line diff-line-num new" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
31
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC31" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="nf" style="color: #900; font-weight: 600;">hash</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">bases</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
32
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC32" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">code</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">bases</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
33
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC33" 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;">bases</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>
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<td class="new_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
34
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC34" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">byte</span> <span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">bases</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">];</span></span>
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35
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC35" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mode</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;">code</span><span class="o" style="font-weight: 600;">&</span><span class="mi" style="color: #099;">31</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
36
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC36" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">hashcodes</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">]!=</span><span class="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="s" style="color: #d14;">"Invalid sequence character: '"</span><span class="o" style="font-weight: 600;">+(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">)</span><span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"'"</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
37
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC37" class="line" lang="java"> <span class="n" style="color: #333;">code</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">code</span><span class="o" style="font-weight: 600;">^</span><span class="n" style="color: #333;">hashcodes</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">mode</span><span class="o" style="font-weight: 600;">];</span></span>
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<td class="new_line diff-line-num new" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
38
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC38" class="line" lang="java"> <span class="n" style="color: #333;">code</span><span class="o" style="font-weight: 600;">=</span><span class="nc" style="color: #458; font-weight: 600;">Long</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">rotateLeft</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">code</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
39
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC39" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
40
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC40" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">code</span><span class="o" style="font-weight: 600;">;</span></span>
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41
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC41" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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42
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC42" class="line" lang="java"> </span>
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<td class="new_line diff-line-num new" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
43
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC43" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="nf" style="color: #900; font-weight: 600;">hash</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Read</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
44
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC44" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="nf" style="color: #900; font-weight: 600;">hash</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="na" style="color: #008080;">bases</span><span class="o" style="font-weight: 600;">);</span></span>
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45
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC45" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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46
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC46" class="line" lang="java"> </span>
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<td class="new_line diff-line-num new" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
47
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC47" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="nf" style="color: #900; font-weight: 600;">hashPair</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Read</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
48
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC48" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">hash</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
49
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<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;">r</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">mate</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="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">;}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
50
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC50" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">hash</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">mate</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC51" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">^</span><span class="nc" style="color: #458; font-weight: 600;">Long</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">rotateLeft</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">);</span></span>
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52
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC52" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
53
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC53" class="line" lang="java"> </span>
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<td class="new_line diff-line-num new" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
54
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC54" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">equalsPaired</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Read</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">Read</span> <span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
55
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC55" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="nf" style="color: #900; font-weight: 600;">equals</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;">b</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">equals</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;">mate</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">mate</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
56
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC56" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
57
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC57" class="line" lang="java"> </span>
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<td class="new_line diff-line-num new" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
58
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC58" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Read</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">Read</span> <span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
59
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<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;">a</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">){</span><span class="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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<td class="new_line diff-line-num new" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
60
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<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;">a</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;">b</span><span class="o" style="font-weight: 600;">==</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
61
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC61" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</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="kc" style="font-weight: 600;">null</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">!=</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
62
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC62" 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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63
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC63" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
64
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC64" 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;">a</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;">b</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="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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<td class="new_line diff-line-num new" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
65
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<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="n" style="color: #333;">a</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="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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66
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC66" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">ab</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;">bases</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">bb</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">bases</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
67
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<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;">ab</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>
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<td class="new_line diff-line-num new" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
68
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<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;">ab</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;">bb</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]){</span><span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
69
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC69" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
70
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC70" 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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<td class="new_line diff-line-num new" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
71
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC71" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
72
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC72" class="line" lang="java"> </span>
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<td class="new_line diff-line-num new" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
73
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC73" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">[][]</span> <span class="n" style="color: #333;">hashcodes</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">makeCodes2</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">32</span><span class="o" style="font-weight: 600;">);</span></span>
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74
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC74" class="line" lang="java"> </span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC75" class="line" lang="java"><span class="o" style="font-weight: 600;">}</span></span></pre></td>
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<a href="https://salsa.debian.org/med-team/bbmap/-/commit/1c662261847da712e5b04b94277f8aa712c37619#5679e4c772d1c2b111dbcd93c6cd1d5a7c0f50e3" style="color: #1068bf; text-decoration: none;"><strong style="font-weight: bold;">current/clump/KmerSort.java</strong></a>
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<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -3,6 +3,7 @@ package clump;</td>
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3
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<td class="new_line diff-line-num" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
3
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC3" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.io.PrintStream</span><span class="o" style="font-weight: 600;">;</span></span>
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4
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<td class="new_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
4
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC4" 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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5
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<td class="new_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
5
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC5" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.Collections</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
6
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC6" 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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6
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<td class="new_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
7
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC7" class="line" lang="java"></span>
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7
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<td class="new_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
8
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC8" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">bloom.KCountArray</span><span class="o" style="font-weight: 600;">;</span></span>
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8
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9
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC9" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">fileIO.ReadWrite</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="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -66,7 +67,8 @@ public abstract class KmerSort {</td>
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<td class="old_line diff-line-num" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
66
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<td class="new_line diff-line-num" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
67
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC67" class="line" lang="java"> </span>
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<td class="old_line diff-line-num" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
67
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<td class="new_line diff-line-num" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
68
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC68" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">cpstring</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;">groups</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;">clumpsProcessedThisPass</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">clumpsProcessedTotal</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
68
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<td class="new_line diff-line-num" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
69
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC69" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">epstring</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;">correctionsTotal</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
69
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<td class="new_line diff-line-num old" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC69" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">dpstring</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;">duplicatesTotal</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
70
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC70" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">efstring</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;">entryFiltered</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
71
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC71" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">dpstring</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;">duplicatesTotal</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">entryFiltered</span><span class="o" style="font-weight: 600;">);</span></span>
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70
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<td class="new_line diff-line-num" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
72
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC72" class="line" lang="java"></span>
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<td class="old_line diff-line-num" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
71
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<td class="new_line diff-line-num" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
73
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC73" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">rostring</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;">readsOut</span><span class="o" style="font-weight: 600;">;</span></span>
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72
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<td class="new_line diff-line-num" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
74
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC74" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">bostring</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;">basesOut</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="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -79,6 +81,7 @@ public abstract class KmerSort {</td>
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<td class="old_line diff-line-num" 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: inherit;" align="right" bgcolor="#fafafa">
79
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<td class="new_line diff-line-num" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
81
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <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;">rpstring2</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;">12</span><span class="o" style="font-weight: 600;">){</span><span class="n" style="color: #333;">rpstring2</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;">rpstring2</span><span class="o" style="font-weight: 600;">;}</span></span>
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<td class="old_line diff-line-num" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
80
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<td class="new_line diff-line-num" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
82
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC82" 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;">cpstring</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;">12</span><span class="o" style="font-weight: 600;">){</span><span class="n" style="color: #333;">cpstring</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;">cpstring</span><span class="o" style="font-weight: 600;">;}</span></span>
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81
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<td class="new_line diff-line-num" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
83
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC83" 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;">epstring</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;">12</span><span class="o" style="font-weight: 600;">){</span><span class="n" style="color: #333;">epstring</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;">epstring</span><span class="o" style="font-weight: 600;">;}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
84
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC84" class="line" lang="java"> <span class="k" style="font-weight: 600;">while</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">efstring</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;">12</span><span class="o" style="font-weight: 600;">){</span><span class="n" style="color: #333;">efstring</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;">efstring</span><span class="o" style="font-weight: 600;">;}</span></span>
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82
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<td class="new_line diff-line-num" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
85
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC85" 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;">dpstring</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;">12</span><span class="o" style="font-weight: 600;">){</span><span class="n" style="color: #333;">dpstring</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;">dpstring</span><span class="o" style="font-weight: 600;">;}</span></span>
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83
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<td class="new_line diff-line-num" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
86
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC86" class="line" lang="java"></span>
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84
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<td class="new_line diff-line-num" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
87
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC87" 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;">rostring</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;">12</span><span class="o" style="font-weight: 600;">){</span><span class="n" style="color: #333;">rostring</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;">rostring</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="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -92,8 +95,11 @@ public abstract class KmerSort {</td>
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<td class="old_line diff-line-num" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
92
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<td class="new_line diff-line-num" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
95
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <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;">correct</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="old_line diff-line-num" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
93
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<td class="new_line diff-line-num" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
96
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC96" class="line" lang="java"> <span class="n" style="color: #333;">outstream</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;">"Errors Corrected: "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">epstring</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
94
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<td class="new_line diff-line-num" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
97
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC97" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="old_line diff-line-num old" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
95
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<td class="new_line diff-line-num old" 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: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<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;">dedupe</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="old_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
98
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<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;">dedupe</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">||</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333;"><span class="idiff right addition" style="background-color: #c7f0d2;">entryfilter</span></span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="old_line diff-line-num" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
96
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<td class="new_line diff-line-num" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
99
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC99" class="line" lang="java"> <span class="n" style="color: #333;">outstream</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;">"Duplicates Found: "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">dpstring</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
100
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<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="n" style="color: #333;">entryfilter</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">verbose</span> <span class="o" style="font-weight: 600;">&&</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="old_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
101
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC101" class="line" lang="java"> <span class="n" style="color: #333;">outstream</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;">" -Entry Filtered: "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">efstring</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
102
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC102" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
97
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<td class="new_line diff-line-num" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
103
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC103" class="line" lang="java"> <span class="n" style="color: #333;">outstream</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;">"Reads Out: "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">rostring</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
98
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<td class="new_line diff-line-num" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
104
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC104" class="line" lang="java"> <span class="n" style="color: #333;">outstream</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;">"Bases Out: "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">bostring</span><span class="o" style="font-weight: 600;">);</span></span>
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99
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<td class="new_line diff-line-num" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
105
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC105" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -271,7 +277,7 @@ public abstract class KmerSort {</td>
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<td class="old_line diff-line-num" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
271
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<td class="new_line diff-line-num" data-linenumber="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
277
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC277" class="line" lang="java"> <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;">FetchThread1</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">alft</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;">FetchThread1</span><span class="o" style="font-weight: 600;">>(</span><span class="n" style="color: #333;">threads</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
272
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<td class="new_line diff-line-num" data-linenumber="278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
278
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC278" 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;">threads</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;">alft</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;">FetchThread1</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;">cris</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">kc</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">unpair</span><span class="o" style="font-weight: 600;">));}</span></span>
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<td class="old_line diff-line-num" data-linenumber="273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
273
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<td class="new_line diff-line-num" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
279
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC279" class="line" lang="java"> </span>
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<td class="old_line diff-line-num old" data-linenumber="274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
274
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<td class="new_line diff-line-num old" data-linenumber="280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC274" class="line" lang="java"> <span class="n" style="color: #333;">readsThisPass</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">memThisPass</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="old_line diff-line-num new" data-linenumber="275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
280
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC280" class="line" lang="java"> <span class="n" style="color: #333;">readsThisPass</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">memThisPass</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;"><span class="idiff left addition" style="background-color: #c7f0d2;">entryFilteredThisPass</span></span><span class="o" style="font-weight: 600;"><span class="idiff right addition" style="background-color: #c7f0d2;">=</span></span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
275
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<td class="new_line diff-line-num" data-linenumber="281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
281
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC281" class="line" lang="java"> </span>
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<td class="old_line diff-line-num" data-linenumber="276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
276
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<td class="new_line diff-line-num" data-linenumber="282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
282
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC282" 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;">verbose</span><span class="o" style="font-weight: 600;">){</span><span class="n" style="color: #333;">outstream</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;">"Starting threads."</span><span class="o" style="font-weight: 600;">);}</span></span>
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<td class="old_line diff-line-num" data-linenumber="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
277
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<td class="new_line diff-line-num" data-linenumber="283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
283
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC283" 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;">FetchThread1</span> <span class="n" style="color: #333;">ht</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">alft</span><span class="o" style="font-weight: 600;">){</span><span class="n" style="color: #333;">ht</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">start</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="289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -289,6 +295,7 @@ public abstract class KmerSort {</td>
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<td class="old_line diff-line-num" data-linenumber="289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
289
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<td class="new_line diff-line-num" data-linenumber="295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
295
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC295" 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="old_line diff-line-num" data-linenumber="290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
290
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<td class="new_line diff-line-num" data-linenumber="296" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
296
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC296" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
291
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<td class="new_line diff-line-num" data-linenumber="297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
297
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC297" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="old_line diff-line-num new" data-linenumber="292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
298
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC298" class="line" lang="java"> <span class="n" style="color: #333;">entryFilteredThisPass</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">ht</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">entryFilteredT</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
292
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<td class="new_line diff-line-num" data-linenumber="299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
299
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC299" class="line" lang="java"> <span class="n" style="color: #333;">readsThisPass</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">ht</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">readsProcessedT</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
293
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<td class="new_line diff-line-num" data-linenumber="300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
300
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC300" class="line" lang="java"> <span class="n" style="color: #333;">basesProcessed</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">ht</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">basesProcessedT</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="294" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
294
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<td class="new_line diff-line-num" data-linenumber="301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
301
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC301" class="line" lang="java"> <span class="n" style="color: #333;">diskProcessed</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">ht</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">diskProcessedT</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="296" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -296,24 +303,28 @@ public abstract class KmerSort {</td>
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<td class="old_line diff-line-num" data-linenumber="296" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
296
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<td class="new_line diff-line-num" data-linenumber="303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
303
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC303" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
297
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<td class="new_line diff-line-num" data-linenumber="304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
304
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC304" class="line" lang="java"> <span class="n" style="color: #333;">readsProcessed</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">readsThisPass</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
298
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<td class="new_line diff-line-num" data-linenumber="305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
305
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC305" class="line" lang="java"> <span class="n" style="color: #333;">memProcessed</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">memThisPass</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
306
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC306" class="line" lang="java"> <span class="n" style="color: #333;">entryFiltered</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">entryFilteredThisPass</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
299
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<td class="new_line diff-line-num" data-linenumber="307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
307
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC307" class="line" lang="java"></span>
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<td class="old_line diff-line-num" data-linenumber="300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
300
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<td class="new_line diff-line-num" data-linenumber="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
308
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC308" 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;">verbose</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;">stop</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Fetch time: "</span><span class="o" style="font-weight: 600;">);}</span></span>
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<td class="old_line diff-line-num" data-linenumber="301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
301
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<td class="new_line diff-line-num" data-linenumber="309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
309
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <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;">verbose</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;">"Closing input stream."</span><span class="o" style="font-weight: 600;">);}</span></span>
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<td class="old_line diff-line-num" data-linenumber="302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
302
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<td class="new_line diff-line-num" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
310
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC310" class="line" lang="java"> <span class="n" style="color: #333;">errorState</span><span class="o" style="font-weight: 600;">=</span><span class="nc" style="color: #458; font-weight: 600;">ReadWrite</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">closeStream</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">cris</span><span class="o" style="font-weight: 600;">)|</span><span class="n" style="color: #333;">errorState</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
303
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<td class="new_line diff-line-num" data-linenumber="311" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
311
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC311" class="line" lang="java"> </span>
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<td class="old_line diff-line-num" data-linenumber="304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
304
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<td class="new_line diff-line-num" data-linenumber="312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
312
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC312" 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;">verbose</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;">start</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Combining thread output."</span><span class="o" style="font-weight: 600;">);}</span></span>
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<td class="old_line diff-line-num old" data-linenumber="305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
305
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<td class="new_line diff-line-num old" data-linenumber="313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC305" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">readsProcessed</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;">MAX_VALUE</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
313
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC313" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">readsLeft</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">readsThisPass</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">entryFilteredThisPass</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
314
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC314" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">slotsLeft</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">cris</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">paired</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;">unpair</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">readsLeft</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;">readsLeft</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
315
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC315" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">slotsLeft</span><span class="o" style="font-weight: 600;"><=</span><span class="nc" style="color: #458; font-weight: 600;">Shared</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">MAX_ARRAY_LEN</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">:</span></span>
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<td class="old_line diff-line-num" data-linenumber="306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
306
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<td class="new_line diff-line-num" data-linenumber="316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
316
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC316" class="line" lang="java"> <span class="s" style="color: #d14;">"\nThe number of reads is greater than 2 billion, which is the limit for a single group. "</span></span>
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<td class="old_line diff-line-num" data-linenumber="307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
307
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<td class="new_line diff-line-num" data-linenumber="317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
317
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC317" class="line" lang="java"> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"\nPlease rerun and manually specify 'groups=7' or similar, "</span></span>
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<td class="old_line diff-line-num" data-linenumber="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
308
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<td class="new_line diff-line-num" data-linenumber="318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
318
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC318" class="line" lang="java"> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"\nsuch that the number of reads per group is less than 2 billion."</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
309
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<td class="new_line diff-line-num old" data-linenumber="319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC309" class="line" lang="java"> <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;">Read</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">list</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;">Read</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;"><span class="idiff left right deletion" style="background-color: #fac5cd;">readsThisPass</span></span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
319
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC319" class="line" lang="java"> <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;">Read</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">list</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;">Read</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 class="idiff left addition" style="background-color: #c7f0d2;">(</span></span><span class="n" style="color: #333;"><span class="idiff addition" style="background-color: #c7f0d2;">slotsLeft</span></span><span class="o" style="font-weight: 600;"><span class="idiff right addition" style="background-color: #c7f0d2;">)</span>);</span></span>
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310
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<td class="new_line diff-line-num" data-linenumber="320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
320
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC320" 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;">threads</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++){</span></span>
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<td class="old_line diff-line-num" data-linenumber="311" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
311
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<td class="new_line diff-line-num" data-linenumber="321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
321
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC321" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">FetchThread1</span> <span class="n" style="color: #333;">ft</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">alft</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">set</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="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
312
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<td class="new_line diff-line-num" data-linenumber="322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
322
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC322" class="line" lang="java"> <span class="n" style="color: #333;">list</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addAll</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ft</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">storage</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
313
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<td class="new_line diff-line-num" data-linenumber="323" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
323
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC323" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
314
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<td class="new_line diff-line-num" data-linenumber="324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
324
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC324" 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;">verbose</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;">stop</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Combine time: "</span><span class="o" style="font-weight: 600;">);}</span></span>
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<td class="old_line diff-line-num" data-linenumber="315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
315
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<td class="new_line diff-line-num" data-linenumber="325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
325
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC325" class="line" lang="java"> </span>
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<td class="old_line diff-line-num old" data-linenumber="316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
316
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<td class="new_line diff-line-num old" data-linenumber="326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC316" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">list</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;">readsThisPass</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">cris</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">paired</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">list</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;">2</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">readsThisPass</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">list</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="s" style="color: #d14;">", "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">readsThisPass</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;">cris</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">paired</span><span class="o" style="font-weight: 600;">();</span></span>
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<td class="old_line diff-line-num new" data-linenumber="317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
326
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC326" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">list</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;">slotsLeft</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">list</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="s" style="color: #d14;">", "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">readsThisPass</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;">readsLeft</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;">slotsLeft</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;">cris</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">paired</span><span class="o" style="font-weight: 600;">();</span></span>
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<td class="old_line diff-line-num new" data-linenumber="317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
327
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC327" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//assert(list.size()==readsLeft || (cris.paired() && list.size()*2==readsLeft)) : list.size()+", "+readsThisPass+", "+readsLeft+", "+cris.paired();</span></span>
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<td class="old_line diff-line-num" data-linenumber="317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
317
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<td class="new_line diff-line-num" data-linenumber="328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
328
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC328" class="line" lang="java"> <span class="n" style="color: #333;">ecco</span><span class="o" style="font-weight: 600;">=</span><span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
318
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<td class="new_line diff-line-num" data-linenumber="329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
329
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC329" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">list</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
319
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330
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC330" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -330,6 +341,7 @@ public abstract class KmerSort {</td>
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330
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<td class="new_line diff-line-num" data-linenumber="341" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
341
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC341" class="line" lang="java"> <span class="n" style="color: #333;">kc</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">kc_</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="331" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
331
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<td class="new_line diff-line-num" data-linenumber="342" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
342
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC342" class="line" lang="java"> <span class="n" style="color: #333;">storage</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;">Read</span><span class="o" style="font-weight: 600;">>();</span></span>
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<td class="old_line diff-line-num" data-linenumber="332" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
332
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<td class="new_line diff-line-num" data-linenumber="343" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
343
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC343" class="line" lang="java"> <span class="n" style="color: #333;">unpairT</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">unpair_</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="344" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
344
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC344" class="line" lang="java"> <span class="n" style="color: #333;">entryFilterTable</span><span class="o" style="font-weight: 600;">=(</span><span class="n" style="color: #333;">entryfilter</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;">Long</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">Read</span><span class="o" style="font-weight: 600;">>()</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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345
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC345" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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347
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -377,6 +389,27 @@ public abstract class KmerSort {</td>
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377
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389
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC389" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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390
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC390" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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379
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391
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC391" class="line" lang="java"> </span>
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<td class="new_line diff-line-num new" data-linenumber="392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
392
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC392" 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;">entryFilterTable</span><span class="o" style="font-weight: 600;">!=</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="393" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
393
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC393" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">removed</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="new_line diff-line-num new" data-linenumber="394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
394
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC394" 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;">reads</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;">i</span><span class="o" style="font-weight: 600;">++){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
395
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC395" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Read</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">reads</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;">i</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
396
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC396" class="line" lang="java"> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">key</span><span class="o" style="font-weight: 600;">=</span><span class="nc" style="color: #458; font-weight: 600;">Hasher</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">hashPair</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="new_line diff-line-num new" data-linenumber="397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
397
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC397" class="line" lang="java"> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">Long</span> <span class="n" style="color: #333;">key2</span><span class="o" style="font-weight: 600;">=</span><span class="nc" style="color: #458; font-weight: 600;">Long</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">valueOf</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">key</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
398
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC398" class="line" lang="java"> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">Read</span> <span class="n" style="color: #333;">old</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">entryFilterTable</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;">key2</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
399
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC399" 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;">old</span><span class="o" style="font-weight: 600;">==</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="old_line diff-line-num new" data-linenumber="380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="400" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
400
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC400" class="line" lang="java"> <span class="n" style="color: #333;">entryFilterTable</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;">key2</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="old_line diff-line-num new" data-linenumber="380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
401
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC401" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span><span class="k" style="font-weight: 600;">else</span><span class="o" style="font-weight: 600;">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
402
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC402" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">same</span><span class="o" style="font-weight: 600;">=</span><span class="nc" style="color: #458; font-weight: 600;">Hasher</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equalsPaired</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;">old</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
403
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC403" 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;">same</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="404" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
404
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC404" class="line" lang="java"> <span class="n" style="color: #333;">removed</span><span class="o" style="font-weight: 600;">++;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
405
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC405" class="line" lang="java"> <span class="n" style="color: #333;">entryFilteredT</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="na" style="color: #008080;">pairCount</span><span class="o" style="font-weight: 600;">();</span></span>
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<td class="new_line diff-line-num new" data-linenumber="406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
406
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC406" class="line" lang="java"> <span class="n" style="color: #333;">reads</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">set</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="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="407" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
407
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC407" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="408" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
408
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC408" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
409
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC409" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
410
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC410" 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;">removed</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="nc" style="color: #458; font-weight: 600;">Tools</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">condenseStrict</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">reads</span><span class="o" style="font-weight: 600;">);}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
411
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC411" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
412
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC412" class="line" lang="java"> </span>
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380
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<td class="new_line diff-line-num" data-linenumber="413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
413
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC413" class="line" lang="java"> <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;">Read</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">hashList</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">reads</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
381
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<td class="new_line diff-line-num" data-linenumber="414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
414
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC414" 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;">paired</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">unpairT</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="old_line diff-line-num" data-linenumber="382" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
382
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<td class="new_line diff-line-num" data-linenumber="415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
415
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC415" class="line" lang="java"> <span class="n" style="color: #333;">hashList</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;">Read</span><span class="o" style="font-weight: 600;">>(</span><span class="n" style="color: #333;">reads</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;">2</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="394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -394,7 +427,7 @@ public abstract class KmerSort {</td>
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<td class="old_line diff-line-num" data-linenumber="394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
394
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<td class="new_line diff-line-num" data-linenumber="427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
427
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC427" class="line" lang="java"> </span>
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<td class="old_line diff-line-num" data-linenumber="395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
395
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<td class="new_line diff-line-num" data-linenumber="428" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
428
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC428" class="line" lang="java"> <span class="n" style="color: #333;">kc</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">hash</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">hashList</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">table</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">minCount</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
396
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<td class="new_line diff-line-num" data-linenumber="429" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
429
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC429" class="line" lang="java"> <span class="n" style="color: #333;">storage</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addAll</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">hashList</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
397
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<td class="new_line diff-line-num old" data-linenumber="430" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC397" class="line" lang="java"> <span class="n" style="color: #333;">cris</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">returnList</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ln</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="430" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
430
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC430" class="line" lang="java"> <span class="n" style="color: #333;">cris</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">returnList</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ln</span><span class="o" style="font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">.</span></span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">id</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">,</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="kc" style="font-weight: 600;"><span class="idiff right addition" style="background-color: #c7f0d2;">false</span></span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
398
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<td class="new_line diff-line-num" data-linenumber="431" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
431
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC431" class="line" lang="java"> <span class="n" style="color: #333;">ln</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">cris</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextList</span><span class="o" style="font-weight: 600;">();</span></span>
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<td class="old_line diff-line-num" data-linenumber="399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
399
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<td class="new_line diff-line-num" data-linenumber="432" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
432
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC432" class="line" lang="java"> <span class="n" style="color: #333;">reads</span><span class="o" style="font-weight: 600;">=(</span><span class="n" style="color: #333;">ln</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;">ln</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">list</span> <span class="o" style="font-weight: 600;">:</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="400" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
400
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<td class="new_line diff-line-num" data-linenumber="433" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
433
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC433" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="416" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="449" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -416,6 +449,8 @@ public abstract class KmerSort {</td>
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<td class="old_line diff-line-num" data-linenumber="416" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
416
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<td class="new_line diff-line-num" data-linenumber="449" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
449
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC449" class="line" lang="java"> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">KmerComparator</span> <span class="n" style="color: #333;">kc</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
417
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<td class="new_line diff-line-num" data-linenumber="450" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
450
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC450" class="line" lang="java"> <span class="kd" style="font-weight: 600;">final</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;">Read</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">storage</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="418" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
418
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<td class="new_line diff-line-num" data-linenumber="451" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
451
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC451" class="line" lang="java"> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">unpairT</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="419" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="452" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
452
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC452" class="line" lang="java"> <span class="kd" style="font-weight: 600;">final</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;">Long</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">Read</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">entryFilterTable</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="419" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="453" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
453
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC453" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">entryFilteredT</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="old_line diff-line-num" data-linenumber="419" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
419
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<td class="new_line diff-line-num" data-linenumber="454" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
454
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC454" class="line" lang="java"> </span>
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<td class="old_line diff-line-num" data-linenumber="420" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
420
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<td class="new_line diff-line-num" data-linenumber="455" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
455
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC455" class="line" lang="java"> <span class="kd" style="font-weight: 600;">protected</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">readsProcessedT</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="old_line diff-line-num" data-linenumber="421" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
421
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<td class="new_line diff-line-num" data-linenumber="456" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
456
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC456" class="line" lang="java"> <span class="kd" style="font-weight: 600;">protected</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">basesProcessedT</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="488" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -488,10 +523,12 @@ public abstract class KmerSort {</td>
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<td class="old_line diff-line-num" data-linenumber="488" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
488
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<td class="new_line diff-line-num" data-linenumber="523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
523
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC523" class="line" lang="java"> <span class="kd" style="font-weight: 600;">protected</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">basesProcessed</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="old_line diff-line-num" data-linenumber="489" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
489
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<td class="new_line diff-line-num" data-linenumber="524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
524
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC524" class="line" lang="java"> <span class="kd" style="font-weight: 600;">protected</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">diskProcessed</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="old_line diff-line-num" data-linenumber="490" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
490
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<td class="new_line diff-line-num" data-linenumber="525" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
525
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC525" class="line" lang="java"> <span class="kd" style="font-weight: 600;">protected</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">memProcessed</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="old_line diff-line-num new" data-linenumber="491" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
526
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC526" class="line" lang="java"> <span class="kd" style="font-weight: 600;">protected</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">entryFiltered</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="old_line diff-line-num" data-linenumber="491" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
491
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<td class="new_line diff-line-num" data-linenumber="527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
527
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC527" class="line" lang="java"></span>
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<td class="old_line diff-line-num" data-linenumber="492" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
492
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<td class="new_line diff-line-num" data-linenumber="528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
528
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC528" class="line" lang="java"> <span class="kd" style="font-weight: 600;">protected</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">readsOut</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="old_line diff-line-num" data-linenumber="493" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
493
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<td class="new_line diff-line-num" data-linenumber="529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
529
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC529" class="line" lang="java"> <span class="kd" style="font-weight: 600;">protected</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">basesOut</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="old_line diff-line-num" data-linenumber="494" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
494
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<td class="new_line diff-line-num" data-linenumber="530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
530
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC530" class="line" lang="java"></span>
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<td class="old_line diff-line-num new" data-linenumber="495" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
531
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC531" class="line" lang="java"> <span class="kd" style="font-weight: 600;">protected</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">entryFilteredThisPass</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="old_line diff-line-num" data-linenumber="495" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
495
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<td class="new_line diff-line-num" data-linenumber="532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
532
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC532" class="line" lang="java"> <span class="kd" style="font-weight: 600;">protected</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">readsThisPass</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="old_line diff-line-num" data-linenumber="496" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
496
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<td class="new_line diff-line-num" data-linenumber="533" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
533
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC533" class="line" lang="java"> <span class="kd" style="font-weight: 600;">protected</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">memThisPass</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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497
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534
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC534" class="line" lang="java"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="520" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="557" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -520,7 +557,9 @@ public abstract class KmerSort {</td>
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520
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<td class="new_line diff-line-num" data-linenumber="557" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
557
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC557" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">unpair</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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521
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<td class="new_line diff-line-num" data-linenumber="558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
558
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC558" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">repair</span><span class="o" style="font-weight: 600;">=</span><span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
522
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<td class="new_line diff-line-num" data-linenumber="559" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
559
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC559" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">namesort</span><span class="o" style="font-weight: 600;">=</span><span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
560
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC560" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">entryfilter</span><span class="o" style="font-weight: 600;">=</span><span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
523
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<td class="new_line diff-line-num" data-linenumber="561" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
561
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC561" class="line" lang="java"> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">parallelSort</span><span class="o" style="font-weight: 600;">=</span><span class="nc" style="color: #458; font-weight: 600;">Shared</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parallelSort</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="562" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
562
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC562" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">memWarned</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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524
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<td class="new_line diff-line-num" data-linenumber="563" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
563
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC563" class="line" lang="java"> </span>
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<td class="old_line diff-line-num" data-linenumber="525" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
525
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<td class="new_line diff-line-num" data-linenumber="564" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
564
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC564" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">useSharedHeader</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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526
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<td class="new_line diff-line-num" data-linenumber="565" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
565
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC565" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">reorderMode</span><span class="o" style="font-weight: 600;">=</span><span class="no" style="color: #008080;">REORDER_FALSE</span><span class="o" style="font-weight: 600;">;</span></span>
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<li id="090a5d3d3431125b6dff5f89cd4cc81c50dd2910">
<a href="https://salsa.debian.org/med-team/bbmap/-/commit/1c662261847da712e5b04b94277f8aa712c37619#090a5d3d3431125b6dff5f89cd4cc81c50dd2910" style="color: #1068bf; text-decoration: none;"><strong style="font-weight: bold;">current/clump/KmerSort1.java</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -119,6 +119,8 @@ public class KmerSort1 extends KmerSort {</td>
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<td class="old_line diff-line-num" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
119
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<td class="new_line diff-line-num" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
119
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC119" class="line" lang="java"> </span>
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<td class="old_line diff-line-num" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
120
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<td class="new_line diff-line-num" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
120
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC120" 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;">a</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"prefilter"</span><span class="o" style="font-weight: 600;">)){</span></span>
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<td class="old_line diff-line-num" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
121
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<td class="new_line diff-line-num" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
121
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC121" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">KmerReduce</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">prefilter</span><span class="o" style="font-weight: 600;">=</span><span class="nc" style="color: #458; font-weight: 600;">Parse</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseBoolean</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
122
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC122" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span><span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</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;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"entryfilter"</span><span class="o" style="font-weight: 600;">)){</span></span>
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<td class="old_line diff-line-num new" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
123
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC123" class="line" lang="java"> <span class="n" style="color: #333;">entryfilter</span><span class="o" style="font-weight: 600;">=</span><span class="nc" style="color: #458; font-weight: 600;">Parse</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseBoolean</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">);</span></span>
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122
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<td class="new_line diff-line-num" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
124
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC124" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span><span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</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;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"groups"</span><span class="o" style="font-weight: 600;">)</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;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"g"</span><span class="o" style="font-weight: 600;">)</span> <span class="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;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"sets"</span><span class="o" style="font-weight: 600;">)</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;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"ways"</span><span class="o" style="font-weight: 600;">)){</span></span>
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123
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<td class="new_line diff-line-num" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
125
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC125" class="line" lang="java"> <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;">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;">b</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
124
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<td class="new_line diff-line-num" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
126
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC126" class="line" lang="java"> <span class="n" style="color: #333;">splitInput</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="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">);</span></span>
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<a href="https://salsa.debian.org/med-team/bbmap/-/commit/1c662261847da712e5b04b94277f8aa712c37619#8abfd720134cdc771f6feb3c373cc6abe51c0f3d" style="color: #1068bf; text-decoration: none;"><strong style="font-weight: bold;">current/clump/KmerSort2.java</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -119,6 +119,8 @@ public class KmerSort2 extends KmerSort {</td>
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<td class="old_line diff-line-num" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
119
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<td class="new_line diff-line-num" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
119
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC119" class="line" lang="java"> </span>
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<td class="old_line diff-line-num" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
120
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<td class="new_line diff-line-num" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
120
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC120" 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;">a</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"prefilter"</span><span class="o" style="font-weight: 600;">)){</span></span>
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<td class="old_line diff-line-num" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
121
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<td class="new_line diff-line-num" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
121
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC121" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">KmerReduce</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">prefilter</span><span class="o" style="font-weight: 600;">=</span><span class="nc" style="color: #458; font-weight: 600;">Parse</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseBoolean</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
122
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC122" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span><span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</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;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"entryfilter"</span><span class="o" style="font-weight: 600;">)){</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
123
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC123" class="line" lang="java"> <span class="n" style="color: #333;">entryfilter</span><span class="o" style="font-weight: 600;">=</span><span class="nc" style="color: #458; font-weight: 600;">Parse</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseBoolean</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">);</span></span>
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122
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<td class="new_line diff-line-num" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
124
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC124" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span><span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</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;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"groups"</span><span class="o" style="font-weight: 600;">)</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;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"g"</span><span class="o" style="font-weight: 600;">)</span> <span class="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;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"sets"</span><span class="o" style="font-weight: 600;">)</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;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"ways"</span><span class="o" style="font-weight: 600;">)){</span></span>
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123
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<td class="new_line diff-line-num" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
125
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC125" class="line" lang="java"> <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;">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;">b</span><span class="o" style="font-weight: 600;">);</span></span>
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124
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<td class="new_line diff-line-num" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
126
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC126" class="line" lang="java"> <span class="n" style="color: #333;">splitInput</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="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">);</span></span>
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<a href="https://salsa.debian.org/med-team/bbmap/-/commit/1c662261847da712e5b04b94277f8aa712c37619#c1f88416f8a24c20df9aefa087b5736241e082fa" style="color: #1068bf; text-decoration: none;"><strong style="font-weight: bold;">current/clump/KmerSort3.java</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -3,6 +3,7 @@ package clump;</td>
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<td class="old_line diff-line-num" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
3
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<td class="new_line diff-line-num" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
3
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC3" 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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4
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<td class="new_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
4
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC4" 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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5
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<td class="new_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
5
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC5" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.Collections</span><span class="o" style="font-weight: 600;">;</span></span>
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6
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC6" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.HashMap</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
6
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<td class="new_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
7
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC7" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.concurrent.SynchronousQueue</span><span class="o" style="font-weight: 600;">;</span></span>
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7
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<td class="new_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
8
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC8" 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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8
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<td class="new_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
9
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC9" class="line" lang="java"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -135,6 +136,8 @@ public class KmerSort3 extends KmerSort {</td>
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<td class="old_line diff-line-num" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
135
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<td class="new_line diff-line-num" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
136
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC136" class="line" lang="java"> </span>
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<td class="old_line diff-line-num" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
136
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<td class="new_line diff-line-num" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
137
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC137" 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;">a</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"prefilter"</span><span class="o" style="font-weight: 600;">)){</span></span>
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<td class="old_line diff-line-num" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
137
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<td class="new_line diff-line-num" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
138
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC138" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">KmerReduce</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">prefilter</span><span class="o" style="font-weight: 600;">=</span><span class="nc" style="color: #458; font-weight: 600;">Parse</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseBoolean</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
139
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC139" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span><span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</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;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"entryfilter"</span><span class="o" style="font-weight: 600;">)){</span></span>
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<td class="old_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
140
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC140" class="line" lang="java"> <span class="n" style="color: #333;">entryfilter</span><span class="o" style="font-weight: 600;">=</span><span class="nc" style="color: #458; font-weight: 600;">Parse</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseBoolean</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
138
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<td class="new_line diff-line-num" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
141
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC141" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span><span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</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;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"groups"</span><span class="o" style="font-weight: 600;">)</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;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"g"</span><span class="o" style="font-weight: 600;">)</span> <span class="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;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"sets"</span><span class="o" style="font-weight: 600;">)</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;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"ways"</span><span class="o" style="font-weight: 600;">)){</span></span>
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<td class="old_line diff-line-num" 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: inherit;" align="right" bgcolor="#fafafa">
139
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<td class="new_line diff-line-num" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
142
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC142" class="line" lang="java"> <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;">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;">b</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
140
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<td class="new_line diff-line-num" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
143
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC143" class="line" lang="java"> <span class="n" style="color: #333;">splitInput</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="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -531,6 +534,7 @@ public class KmerSort3 extends KmerSort {</td>
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<td class="old_line diff-line-num" data-linenumber="531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
531
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<td class="new_line diff-line-num" data-linenumber="534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
534
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC534" 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="nf" style="color: #900; font-weight: 600;">closeFetchThread3s</span><span class="o" style="font-weight: 600;">(</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;">FetchThread3</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">alft</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="old_line diff-line-num" data-linenumber="532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
532
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<td class="new_line diff-line-num" data-linenumber="535" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
535
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC535" class="line" lang="java"> <span class="n" style="color: #333;">readsThisPass</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="old_line diff-line-num" data-linenumber="533" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
533
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<td class="new_line diff-line-num" data-linenumber="536" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
536
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC536" class="line" lang="java"> <span class="n" style="color: #333;">memThisPass</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="old_line diff-line-num new" data-linenumber="534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="537" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
537
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC537" class="line" lang="java"> <span class="n" style="color: #333;">entryFilteredThisPass</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="old_line diff-line-num" data-linenumber="534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
534
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<td class="new_line diff-line-num" data-linenumber="538" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
538
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC538" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/* Wait for threads to die */</span></span>
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<td class="old_line diff-line-num" data-linenumber="535" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
535
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<td class="new_line diff-line-num" data-linenumber="539" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
539
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC539" 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;">FetchThread3</span> <span class="n" style="color: #333;">ft</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">alft</span><span class="o" style="font-weight: 600;">){</span></span>
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536
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540
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC540" class="line" lang="java"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="542" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="546" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -542,6 +546,7 @@ public class KmerSort3 extends KmerSort {</td>
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<td class="old_line diff-line-num" data-linenumber="542" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
542
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<td class="new_line diff-line-num" data-linenumber="546" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
546
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC546" 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="old_line diff-line-num" data-linenumber="543" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
543
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<td class="new_line diff-line-num" data-linenumber="547" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
547
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC547" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="544" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
544
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<td class="new_line diff-line-num" data-linenumber="548" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
548
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC548" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="old_line diff-line-num new" data-linenumber="545" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="549" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
549
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC549" class="line" lang="java"> <span class="n" style="color: #333;">entryFilteredThisPass</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">ft</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">entryFilteredT</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="545" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
545
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<td class="new_line diff-line-num" data-linenumber="550" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
550
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC550" class="line" lang="java"> <span class="n" style="color: #333;">readsThisPass</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">ft</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">readsProcessedT</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="546" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
546
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<td class="new_line diff-line-num" data-linenumber="551" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
551
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC551" class="line" lang="java"> <span class="n" style="color: #333;">basesProcessed</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">ft</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">basesProcessedT</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="547" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
547
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<td class="new_line diff-line-num" data-linenumber="552" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
552
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC552" class="line" lang="java"> <span class="n" style="color: #333;">diskProcessed</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">ft</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">diskProcessedT</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="549" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="554" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -549,6 +554,7 @@ public class KmerSort3 extends KmerSort {</td>
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<td class="old_line diff-line-num" data-linenumber="549" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
549
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<td class="new_line diff-line-num" data-linenumber="554" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
554
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC554" class="line" lang="java"> </span>
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<td class="old_line diff-line-num" data-linenumber="550" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
550
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<td class="new_line diff-line-num" data-linenumber="555" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
555
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC555" class="line" lang="java"> <span class="n" style="color: #333;">errorState</span><span class="o" style="font-weight: 600;">|=</span><span class="n" style="color: #333;">ft</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">errorStateT</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="551" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
551
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<td class="new_line diff-line-num" data-linenumber="556" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
556
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC556" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="old_line diff-line-num new" data-linenumber="552" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="557" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
557
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC557" class="line" lang="java"> <span class="n" style="color: #333;">entryFiltered</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">entryFilteredThisPass</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="552" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
552
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<td class="new_line diff-line-num" data-linenumber="558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
558
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC558" class="line" lang="java"> <span class="n" style="color: #333;">readsProcessed</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">readsThisPass</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="553" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
553
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<td class="new_line diff-line-num" data-linenumber="559" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
559
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC559" class="line" lang="java"> <span class="n" style="color: #333;">memProcessed</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">memThisPass</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC560" class="line" lang="java"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="627" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -627,27 +633,46 @@ public class KmerSort3 extends KmerSort {</td>
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627
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<td class="new_line diff-line-num" data-linenumber="633" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
633
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC633" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// outstream.println("totalMem="+totalMem+", Shared.memFree()="+Shared.memFree()+", Shared.memUsed()="+Shared.memUsed());</span></span>
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628
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<td class="new_line diff-line-num" data-linenumber="634" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
634
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC634" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// outstream.println("fileSize="+fileSize+", "+"fileMem="+fileMem+", "+"memRatio="+memRatio+", ");</span></span>
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629
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<td class="new_line diff-line-num" data-linenumber="635" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
635
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC635" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// outstream.println((size-1000>expectedSizePerGroup*3)+", "+(expectedMem*3>totalMem));</span></span>
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<td class="old_line diff-line-num old" data-linenumber="630" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
630
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<td class="new_line diff-line-num old" data-linenumber="636" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC630" class="line" lang="java"><span class="idiff left right deletion" style="background-color: #fac5cd;"> </span></span>
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<td class="new_line diff-line-num new" data-linenumber="636" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
636
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC636" class="line" lang="java"></span>
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631
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<td class="new_line diff-line-num" data-linenumber="637" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
637
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC637" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//TODO: This could also be based on the number of FetchThreads.</span></span>
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632
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC632" class="line" lang="java"> </span>
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633
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<td class="new_line diff-line-num" data-linenumber="638" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
638
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC638" 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;">expectedMem</span><span class="o" style="font-weight: 600;">></span><span class="mf" style="color: #099;">0.3</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">totalMem</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fileMem</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;">fileMem</span><span class="o" style="font-weight: 600;">></span><span class="mf" style="color: #099;">0.8</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">totalMem</span><span class="o" style="font-weight: 600;">)){</span></span>
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634
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<td class="new_line diff-line-num old" data-linenumber="639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC634" class="line" lang="java"> <span class="n" style="color: #333;">outstream</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;">"\n*** Warning ***\n"</span></span>
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635
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<td class="new_line diff-line-num old" data-linenumber="639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC635" class="line" lang="java"> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"A temp file may be too big to store in memory, due to uneven splitting:"</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
639
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC639" class="line" lang="java"> <span class="kd" style="font-weight: 600;">synchronized</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getClass</span><span class="o" style="font-weight: 600;">()){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="640" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
640
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC640" 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;">memWarned</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="641" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
641
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC641" class="line" lang="java"> <span class="n" style="color: #333;">outstream</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;">"\n*** Warning ***\n"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="642" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
642
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC642" class="line" lang="java"> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"A temp file may be too big to store in memory, due to uneven splitting:"</span><span class="o" style="font-weight: 600;">);</span></span>
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636
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643
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC643" class="line" lang="java"></span>
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637
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC637" class="line" lang="java"> <span class="n" style="color: #333;">outstream</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;">"expectedMem="</span><span class="o" style="font-weight: 600;">+((</span><span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">)</span><span class="n" style="color: #333;">expectedMem</span><span class="o" style="font-weight: 600;">)+</span><span class="s" style="color: #d14;">", fileMem="</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">fileMem</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">", available="</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">totalMem</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="638" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
638
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<td class="new_line diff-line-num old" data-linenumber="644" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC638" class="line" lang="java"></span>
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<td class="old_line diff-line-num old" data-linenumber="639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
639
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<td class="new_line diff-line-num old" data-linenumber="644" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC639" 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;">repair</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">namesort</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="old_line diff-line-num old" data-linenumber="640" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
640
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<td class="new_line diff-line-num old" data-linenumber="644" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC640" class="line" lang="java"> <span class="n" style="color: #333;">outstream</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 cannot be streamed to output unaltered because "</span><span class="o" style="font-weight: 600;">+(</span><span class="n" style="color: #333;">namesort</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">" namesort=t"</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"repair=t"</span><span class="o" style="font-weight: 600;">));</span></span>
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<td class="old_line diff-line-num old" data-linenumber="641" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
641
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<td class="new_line diff-line-num old" data-linenumber="644" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC641" class="line" lang="java"> <span class="n" style="color: #333;">outstream</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;">"If this causes the program to crash, please re-run with more memory or groups.\n"</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="642" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
642
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<td class="new_line diff-line-num old" data-linenumber="644" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC642" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span><span class="k" style="font-weight: 600;">else</span><span class="o" style="font-weight: 600;">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="643" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
643
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<td class="new_line diff-line-num old" data-linenumber="644" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC643" class="line" lang="java"> <span class="n" style="color: #333;">outstream</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>
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<td class="old_line diff-line-num old" data-linenumber="644" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
644
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<td class="new_line diff-line-num old" data-linenumber="644" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC644" class="line" lang="java"> <span class="s" style="color: #d14;">"It will be streamed to output unaltered.\n"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
645
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<td class="new_line diff-line-num old" data-linenumber="644" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC645" class="line" lang="java"> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"To avoid this behavior, increase memory or increase groups.\n"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="646" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
646
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<td class="new_line diff-line-num old" data-linenumber="644" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC646" class="line" lang="java"> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"Set the flag forceprocess=t to disable this check.\n"</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="647" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
647
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<td class="new_line diff-line-num old" data-linenumber="644" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC647" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// Timer t=new Timer();</span></span>
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<td class="old_line diff-line-num old" data-linenumber="648" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
648
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<td class="new_line diff-line-num old" data-linenumber="644" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC648" class="line" lang="java"> <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;">Read</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">list</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">streamNext_inner</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">cris</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="649" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
649
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<td class="new_line diff-line-num old" data-linenumber="644" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC649" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// t.stop("Stream time: ");</span></span>
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<td class="old_line diff-line-num old" data-linenumber="650" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
650
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<td class="new_line diff-line-num old" data-linenumber="644" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC650" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">list</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="651" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="644" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
644
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC644" class="line" lang="java"> <span class="n" style="color: #333;">outstream</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;">"expectedMem="</span><span class="o" style="font-weight: 600;">+((</span><span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">)</span><span class="n" style="color: #333;">expectedMem</span><span class="o" style="font-weight: 600;">)+</span><span class="s" style="color: #d14;">", fileMem="</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">fileMem</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">", available="</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">totalMem</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
645
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC645" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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646
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC646" 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;">entryfilter</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="647" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
647
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC647" 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;">memWarned</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="648" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
648
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC648" class="line" lang="java"> <span class="n" style="color: #333;">outstream</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>
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<td class="old_line diff-line-num new" data-linenumber="651" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="649" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
649
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC649" class="line" lang="java"> <span class="s" style="color: #d14;">"If the program crashes, increase memory or manually increase groups.\n"</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="650" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
650
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC650" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="651" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
651
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC651" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span><span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">dedupe</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;">Clump</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">opticalOnly</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="652" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
652
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC652" 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;">memWarned</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="653" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
653
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC653" class="line" lang="java"> <span class="n" style="color: #333;">outstream</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>
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<td class="old_line diff-line-num new" data-linenumber="651" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="654" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
654
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC654" class="line" lang="java"> <span class="s" style="color: #d14;">"entryfilter is automatically being set to true to reduce memory load while removing duplicates.\n"</span></span>
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<td class="old_line diff-line-num new" data-linenumber="651" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="655" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
655
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC655" class="line" lang="java"> <span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"If the program crashes, increase memory or manually increase groups.\n"</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="656" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
656
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC656" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="old_line diff-line-num new" data-linenumber="651" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="657" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
657
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC657" class="line" lang="java"> <span class="n" style="color: #333;">entryfilter</span><span class="o" style="font-weight: 600;">=</span><span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="658" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
658
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC658" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span><span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">repair</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">namesort</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="659" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
659
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC659" 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;">memWarned</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="old_line diff-line-num new" data-linenumber="651" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="660" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
660
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC660" class="line" lang="java"> <span class="n" style="color: #333;">outstream</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 cannot be streamed to output unaltered because "</span><span class="o" style="font-weight: 600;">+(</span><span class="n" style="color: #333;">namesort</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">" namesort=t"</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"repair=t"</span><span class="o" style="font-weight: 600;">));</span></span>
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<td class="new_line diff-line-num new" data-linenumber="661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
661
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC661" class="line" lang="java"> <span class="n" style="color: #333;">outstream</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;">"If this causes the program to crash, please re-run with more memory or groups.\n"</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
662
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC662" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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663
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC663" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span><span class="k" style="font-weight: 600;">else</span><span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="664" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
664
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC664" 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;">memWarned</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="665" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
665
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC665" class="line" lang="java"> <span class="n" style="color: #333;">outstream</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>
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<td class="new_line diff-line-num new" data-linenumber="666" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
666
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC666" class="line" lang="java"> <span class="s" style="color: #d14;">"It will be streamed to output unaltered.\n"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="667" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
667
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC667" class="line" lang="java"> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"To avoid this behavior, increase memory or increase groups.\n"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="668" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
668
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC668" class="line" lang="java"> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"Set the flag forceprocess=t to disable this check.\n"</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="669" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
669
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC669" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="670" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
670
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC670" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Timer t=new Timer();</span></span>
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<td class="new_line diff-line-num new" data-linenumber="671" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
671
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC671" class="line" lang="java"> <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;">Read</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">list</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">streamNext_inner</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">cris</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="672" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
672
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC672" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// t.stop("Stream time: ");</span></span>
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<td class="new_line diff-line-num new" data-linenumber="673" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
673
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC673" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">list</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="674" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
674
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC674" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="675" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
675
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC675" class="line" lang="java"> <span class="n" style="color: #333;">memWarned</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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651
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676
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC676" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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652
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677
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC677" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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653
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678
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC678" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="673" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="698" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -673,7 +698,7 @@ public class KmerSort3 extends KmerSort {</td>
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673
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<td class="new_line diff-line-num" data-linenumber="698" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
698
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC698" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// if(verbose){t.start("Making hash threads.");}</span></span>
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674
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699
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC699" class="line" lang="java"> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">subthreads</span><span class="o" style="font-weight: 600;">=</span><span class="nc" style="color: #458; font-weight: 600;">Tools</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">mid</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="nc" style="color: #458; font-weight: 600;">Shared</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">threads</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="mi" style="color: #099;">8</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="675" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
675
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<td class="new_line diff-line-num" data-linenumber="700" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
700
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC700" class="line" lang="java"> <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;">FetchSubThread</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">alht</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;">FetchSubThread</span><span class="o" style="font-weight: 600;">>(</span><span class="n" style="color: #333;">subthreads</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="676" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
676
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<td class="new_line diff-line-num old" data-linenumber="701" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC676" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">readsThisGroup</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;">memThisGroup</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="old_line diff-line-num new" data-linenumber="677" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="701" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
701
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC701" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">readsThisGroup</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;">memThisGroup</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">,</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333;"><span class="idiff addition" style="background-color: #c7f0d2;">entryFilteredThisGroup</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">=</span></span><span class="mi" style="color: #099;"><span class="idiff right addition" style="background-color: #c7f0d2;">0</span></span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="677" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
677
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<td class="new_line diff-line-num" data-linenumber="702" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
702
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC702" 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;">subthreads</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;">alht</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;">FetchSubThread</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;">cris</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">kc</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">unpair</span><span class="o" style="font-weight: 600;">));}</span></span>
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<td class="old_line diff-line-num" data-linenumber="678" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
678
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<td class="new_line diff-line-num" data-linenumber="703" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
703
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC703" class="line" lang="java"> </span>
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<td class="old_line diff-line-num" data-linenumber="679" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
679
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<td class="new_line diff-line-num" data-linenumber="704" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
704
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC704" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// if(verbose){outstream.println("Starting threads.");}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="691" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="716" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -691,11 +716,13 @@ public class KmerSort3 extends KmerSort {</td>
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<td class="old_line diff-line-num" data-linenumber="691" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
691
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<td class="new_line diff-line-num" data-linenumber="716" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
716
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC716" 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="old_line diff-line-num" data-linenumber="692" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
692
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<td class="new_line diff-line-num" data-linenumber="717" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
717
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC717" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="693" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
693
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<td class="new_line diff-line-num" data-linenumber="718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
718
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC718" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="old_line diff-line-num new" data-linenumber="694" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
719
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC719" class="line" lang="java"> <span class="n" style="color: #333;">entryFilteredThisGroup</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">ht</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">entryFilteredT</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="694" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
694
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<td class="new_line diff-line-num" data-linenumber="720" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
720
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC720" class="line" lang="java"> <span class="n" style="color: #333;">readsThisGroup</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">ht</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">readsProcessedST</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="695" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
695
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<td class="new_line diff-line-num" data-linenumber="721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
721
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC721" class="line" lang="java"> <span class="n" style="color: #333;">basesProcessedT</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">ht</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">basesProcessedST</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="696" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
696
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<td class="new_line diff-line-num" data-linenumber="722" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
722
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC722" class="line" lang="java"> <span class="n" style="color: #333;">diskProcessedT</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">ht</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">diskProcessedST</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="697" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
697
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<td class="new_line diff-line-num" data-linenumber="723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
723
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC723" class="line" lang="java"> <span class="n" style="color: #333;">memThisGroup</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">ht</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">memProcessedST</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="698" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
698
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724
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC724" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="old_line diff-line-num new" data-linenumber="699" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="725" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
725
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC725" class="line" lang="java"> <span class="n" style="color: #333;">entryFilteredT</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">entryFilteredThisGroup</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="699" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
699
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<td class="new_line diff-line-num" data-linenumber="726" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
726
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC726" class="line" lang="java"> <span class="n" style="color: #333;">readsProcessedT</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">readsThisGroup</span><span class="o" style="font-weight: 600;">;</span></span>
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700
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<td class="new_line diff-line-num" data-linenumber="727" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
727
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC727" class="line" lang="java"> <span class="n" style="color: #333;">memProcessedT</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">memThisGroup</span><span class="o" style="font-weight: 600;">;</span></span>
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701
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728
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC728" class="line" lang="java"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="704" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="731" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -704,13 +731,15 @@ public class KmerSort3 extends KmerSort {</td>
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<td class="old_line diff-line-num" data-linenumber="704" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
704
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<td class="new_line diff-line-num" data-linenumber="731" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
731
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC731" class="line" lang="java"> <span class="n" style="color: #333;">errorStateT</span><span class="o" style="font-weight: 600;">=</span><span class="nc" style="color: #458; font-weight: 600;">ReadWrite</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">closeStream</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">cris</span><span class="o" style="font-weight: 600;">)|</span><span class="n" style="color: #333;">errorStateT</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="705" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
705
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<td class="new_line diff-line-num" data-linenumber="732" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
732
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC732" class="line" lang="java"> </span>
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<td class="old_line diff-line-num" data-linenumber="706" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
706
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<td class="new_line diff-line-num" data-linenumber="733" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
733
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC733" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// if(verbose){t.start("Combining thread output.");}</span></span>
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<td class="old_line diff-line-num old" data-linenumber="707" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
707
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<td class="new_line diff-line-num old" data-linenumber="734" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC707" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">readsProcessedT</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;">MAX_VALUE</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">readsProcessedT</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="old_line diff-line-num old" data-linenumber="708" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
708
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<td class="new_line diff-line-num old" data-linenumber="734" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC708" class="line" lang="java"> <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;">Read</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">list</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;">Read</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;">readsThisGroup</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="709" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="734" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
734
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC734" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">readsLeft</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">readsThisGroup</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">entryFilteredThisGroup</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="709" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="735" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
735
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC735" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">slotsLeft</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">cris</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">paired</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;">unpair</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">readsLeft</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;">readsLeft</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="709" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="736" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
736
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC736" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">slotsLeft</span><span class="o" style="font-weight: 600;"><=</span><span class="nc" style="color: #458; font-weight: 600;">Shared</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">MAX_ARRAY_LEN</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">readsProcessedT</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="new_line diff-line-num new" data-linenumber="737" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
737
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC737" class="line" lang="java"> <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;">Read</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">list</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;">Read</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;">slotsLeft</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="709" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
709
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<td class="new_line diff-line-num" data-linenumber="738" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
738
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC738" 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;">subthreads</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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710
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<td class="new_line diff-line-num" data-linenumber="739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
739
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC739" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">FetchSubThread</span> <span class="n" style="color: #333;">ht</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">alht</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">set</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="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="711" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
711
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<td class="new_line diff-line-num" data-linenumber="740" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
740
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC740" class="line" lang="java"> <span class="n" style="color: #333;">list</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addAll</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ht</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">storage</span><span class="o" style="font-weight: 600;">);</span></span>
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712
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<td class="new_line diff-line-num" data-linenumber="741" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
741
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC741" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="old_line diff-line-num old" data-linenumber="713" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
713
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<td class="new_line diff-line-num old" data-linenumber="742" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC713" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">list</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;"><span class="idiff left deletion" style="background-color: #fac5cd;">readsThisGroup</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">||</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">(</span></span><span class="n" style="color: #333;"><span class="idiff deletion" style="background-color: #fac5cd;">cris</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">.</span></span><span class="na" style="color: #008080;"><span class="idiff deletion" style="background-color: #fac5cd;">paired</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">()</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">&&</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333;"><span class="idiff deletion" style="background-color: #fac5cd;">list</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">.</span></span><span class="na" style="color: #008080;"><span class="idiff deletion" style="background-color: #fac5cd;">size</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">()*</span></span><span class="mi" style="color: #099;"><span class="idiff deletion" style="background-color: #fac5cd;">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">==</span></span><span class="n" style="color: #333;"><span class="idiff deletion" style="background-color: #fac5cd;">readsThisGroup</span></span><span class="o" style="font-weight: 600;"><span class="idiff right deletion" style="background-color: #fac5cd;">)</span>)</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">list</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="s" style="color: #d14;">", "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">readsThisGroup</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;">cris</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">paired</span><span class="o" style="font-weight: 600;">();</span></span>
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<td class="old_line diff-line-num new" data-linenumber="714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="742" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
742
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC742" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">list</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;"><span class="idiff left addition" style="background-color: #c7f0d2;">slotsLeft</span></span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">list</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="s" style="color: #d14;">", "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">readsThisGroup</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">", <span class="idiff addition" style="background-color: #c7f0d2;">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">+</span></span><span class="n" style="color: #333;"><span class="idiff addition" style="background-color: #c7f0d2;">slotsLeft</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">+</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">", </span>"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">cris</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">paired</span><span class="o" style="font-weight: 600;">();</span></span>
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<td class="old_line diff-line-num" data-linenumber="714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
714
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<td class="new_line diff-line-num" data-linenumber="743" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
743
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC743" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// if(verbose){t.stop("Combine time: ");}</span></span>
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715
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<td class="new_line diff-line-num" data-linenumber="744" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
744
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC744" class="line" lang="java"> </span>
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716
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<td class="new_line diff-line-num" data-linenumber="745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
745
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC745" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// if(verbose){t.start("Sorting.");}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="753" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -724,7 +753,8 @@ public class KmerSort3 extends KmerSort {</td>
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<td class="old_line diff-line-num" data-linenumber="724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
724
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<td class="new_line diff-line-num" data-linenumber="753" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
753
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC753" class="line" lang="java"> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">AtomicInteger</span> <span class="n" style="color: #333;">nextGroup</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="725" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
725
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<td class="new_line diff-line-num" data-linenumber="754" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
754
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC754" class="line" lang="java"> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">KmerComparator</span> <span class="n" style="color: #333;">kc</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="726" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
726
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<td class="new_line diff-line-num" data-linenumber="755" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
755
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC755" class="line" lang="java"> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">ConcurrentReadOutputStream</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">rosa</span><span class="o" style="font-weight: 600;">;</span></span>
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727
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<td class="new_line diff-line-num old" data-linenumber="756" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC727" class="line" lang="java"> </span>
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<td class="new_line diff-line-num new" data-linenumber="756" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
756
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC756" class="line" lang="java"></span>
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<td class="new_line diff-line-num new" data-linenumber="757" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
757
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC757" class="line" lang="java"> <span class="kd" style="font-weight: 600;">protected</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">entryFilteredT</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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728
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<td class="new_line diff-line-num" data-linenumber="758" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
758
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC758" class="line" lang="java"> <span class="kd" style="font-weight: 600;">protected</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">readsProcessedT</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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729
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<td class="new_line diff-line-num" data-linenumber="759" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
759
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC759" class="line" lang="java"> <span class="kd" style="font-weight: 600;">protected</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">basesProcessedT</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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730
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760
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC760" class="line" lang="java"> <span class="kd" style="font-weight: 600;">protected</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">diskProcessedT</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="740" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -740,6 +770,7 @@ public class KmerSort3 extends KmerSort {</td>
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740
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<td class="new_line diff-line-num" data-linenumber="770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
770
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC770" class="line" lang="java"> <span class="n" style="color: #333;">kcT</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">kc_</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="741" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
741
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<td class="new_line diff-line-num" data-linenumber="771" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
771
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC771" class="line" lang="java"> <span class="n" style="color: #333;">storage</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;">Read</span><span class="o" style="font-weight: 600;">>();</span></span>
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<td class="old_line diff-line-num" data-linenumber="742" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
742
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<td class="new_line diff-line-num" data-linenumber="772" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
772
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC772" class="line" lang="java"> <span class="n" style="color: #333;">unpairT</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">unpair_</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="743" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="773" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
773
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC773" class="line" lang="java"> <span class="n" style="color: #333;">entryFilterTable</span><span class="o" style="font-weight: 600;">=(</span><span class="n" style="color: #333;">entryfilter</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;">Long</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">Read</span><span class="o" style="font-weight: 600;">>()</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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743
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774
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC774" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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775
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC775" class="line" lang="java"> </span>
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776
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC776" class="line" lang="java"> <span class="nd">@Override</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="783" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="814" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -783,6 +814,27 @@ public class KmerSort3 extends KmerSort {</td>
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783
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814
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC814" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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784
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<td class="new_line diff-line-num" data-linenumber="815" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
815
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC815" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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785
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816
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC816" class="line" lang="java"> </span>
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<td class="old_line diff-line-num new" data-linenumber="786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="817" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
817
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC817" 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;">entryFilterTable</span><span class="o" style="font-weight: 600;">!=</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="818" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
818
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC818" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">removed</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="new_line diff-line-num new" data-linenumber="819" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
819
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC819" 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;">reads</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;">i</span><span class="o" style="font-weight: 600;">++){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="820" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
820
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC820" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Read</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">reads</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;">i</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="821" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
821
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC821" class="line" lang="java"> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">key</span><span class="o" style="font-weight: 600;">=</span><span class="nc" style="color: #458; font-weight: 600;">Hasher</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">hashPair</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="old_line diff-line-num new" data-linenumber="786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="822" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
822
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC822" class="line" lang="java"> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">Long</span> <span class="n" style="color: #333;">key2</span><span class="o" style="font-weight: 600;">=</span><span class="nc" style="color: #458; font-weight: 600;">Long</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">valueOf</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">key</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
823
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC823" class="line" lang="java"> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">Read</span> <span class="n" style="color: #333;">old</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">entryFilterTable</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;">key2</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="824" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
824
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC824" 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;">old</span><span class="o" style="font-weight: 600;">==</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="old_line diff-line-num new" data-linenumber="786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="825" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
825
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC825" class="line" lang="java"> <span class="n" style="color: #333;">entryFilterTable</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;">key2</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="old_line diff-line-num new" data-linenumber="786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="826" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
826
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC826" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span><span class="k" style="font-weight: 600;">else</span><span class="o" style="font-weight: 600;">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="827" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
827
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC827" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">same</span><span class="o" style="font-weight: 600;">=</span><span class="nc" style="color: #458; font-weight: 600;">Hasher</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equalsPaired</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;">old</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="828" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
828
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC828" 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;">same</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="old_line diff-line-num new" data-linenumber="786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="829" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
829
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC829" class="line" lang="java"> <span class="n" style="color: #333;">removed</span><span class="o" style="font-weight: 600;">++;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="830" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
830
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC830" class="line" lang="java"> <span class="n" style="color: #333;">entryFilteredT</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="na" style="color: #008080;">pairCount</span><span class="o" style="font-weight: 600;">();</span></span>
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<td class="old_line diff-line-num new" data-linenumber="786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="831" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
831
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC831" class="line" lang="java"> <span class="n" style="color: #333;">reads</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">set</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="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="832" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
832
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC832" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="833" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
833
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC833" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="834" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
834
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC834" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="old_line diff-line-num new" data-linenumber="786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="835" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
835
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC835" 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;">removed</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="nc" style="color: #458; font-weight: 600;">Tools</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">condenseStrict</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">reads</span><span class="o" style="font-weight: 600;">);}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="836" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
836
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC836" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="old_line diff-line-num new" data-linenumber="786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="837" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
837
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC837" class="line" lang="java"> </span>
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<td class="old_line diff-line-num" data-linenumber="786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
786
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<td class="new_line diff-line-num" data-linenumber="838" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
838
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC838" class="line" lang="java"> <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;">Read</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">hashList</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">reads</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
787
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<td class="new_line diff-line-num" data-linenumber="839" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
839
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC839" 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;">paired</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">unpairT</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="old_line diff-line-num" data-linenumber="788" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
788
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<td class="new_line diff-line-num" data-linenumber="840" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
840
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC840" class="line" lang="java"> <span class="n" style="color: #333;">hashList</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;">Read</span><span class="o" style="font-weight: 600;">>(</span><span class="n" style="color: #333;">reads</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;">2</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="800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="852" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -800,7 +852,7 @@ public class KmerSort3 extends KmerSort {</td>
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<td class="old_line diff-line-num" data-linenumber="800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
800
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<td class="new_line diff-line-num" data-linenumber="852" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
852
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC852" class="line" lang="java"> </span>
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<td class="old_line diff-line-num" data-linenumber="801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
801
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<td class="new_line diff-line-num" data-linenumber="853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
853
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC853" class="line" lang="java"> <span class="n" style="color: #333;">kcT</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">hash</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">hashList</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">table</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">minCount</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="802" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
802
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<td class="new_line diff-line-num" data-linenumber="854" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
854
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC854" class="line" lang="java"> <span class="n" style="color: #333;">storage</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addAll</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">hashList</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="803" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
803
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<td class="new_line diff-line-num old" data-linenumber="855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC803" class="line" lang="java"> <span class="n" style="color: #333;">cris</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">returnList</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ln</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="804" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
855
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC855" class="line" lang="java"> <span class="n" style="color: #333;">cris</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">returnList</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ln</span><span class="o" style="font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">.</span></span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">id</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">,</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="kc" style="font-weight: 600;"><span class="idiff right addition" style="background-color: #c7f0d2;">false</span></span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="804" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
804
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<td class="new_line diff-line-num" data-linenumber="856" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
856
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC856" class="line" lang="java"> <span class="n" style="color: #333;">ln</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">cris</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextList</span><span class="o" style="font-weight: 600;">();</span></span>
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<td class="old_line diff-line-num" data-linenumber="805" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
805
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<td class="new_line diff-line-num" data-linenumber="857" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
857
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC857" class="line" lang="java"> <span class="n" style="color: #333;">reads</span><span class="o" style="font-weight: 600;">=(</span><span class="n" style="color: #333;">ln</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;">ln</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">list</span> <span class="o" style="font-weight: 600;">:</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="806" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
806
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<td class="new_line diff-line-num" data-linenumber="858" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
858
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC858" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="822" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="874" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -822,6 +874,8 @@ public class KmerSort3 extends KmerSort {</td>
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<td class="old_line diff-line-num" data-linenumber="822" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
822
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<td class="new_line diff-line-num" data-linenumber="874" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
874
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC874" class="line" lang="java"> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">KmerComparator</span> <span class="n" style="color: #333;">kcT</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
823
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<td class="new_line diff-line-num" data-linenumber="875" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
875
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC875" class="line" lang="java"> <span class="kd" style="font-weight: 600;">final</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;">Read</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">storage</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="824" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
824
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<td class="new_line diff-line-num" data-linenumber="876" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
876
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC876" class="line" lang="java"> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">unpairT</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="825" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="877" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
877
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC877" class="line" lang="java"> <span class="kd" style="font-weight: 600;">final</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;">Long</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">Read</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">entryFilterTable</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="825" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
878
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC878" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">entryFilteredT</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="old_line diff-line-num" data-linenumber="825" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
825
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<td class="new_line diff-line-num" data-linenumber="879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
879
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC879" class="line" lang="java"></span>
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<td class="old_line diff-line-num" data-linenumber="826" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
826
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<td class="new_line diff-line-num" data-linenumber="880" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
880
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC880" class="line" lang="java"> <span class="kd" style="font-weight: 600;">protected</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">readsProcessedST</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="old_line diff-line-num" data-linenumber="827" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
827
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<td class="new_line diff-line-num" data-linenumber="881" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
881
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC881" class="line" lang="java"> <span class="kd" style="font-weight: 600;">protected</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">basesProcessedST</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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<a href="https://salsa.debian.org/med-team/bbmap/-/commit/1c662261847da712e5b04b94277f8aa712c37619#8b67bed9478adfa01af5effee08f3ea398d80963" style="color: #1068bf; text-decoration: none;"><strong style="font-weight: bold;">current/clump/KmerSplit.java</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -123,6 +123,8 @@ public class KmerSplit {</td>
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<td class="old_line diff-line-num" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
123
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<td class="new_line diff-line-num" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
123
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC123" class="line" lang="java"> </span>
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<td class="old_line diff-line-num" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
124
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<td class="new_line diff-line-num" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
124
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC124" 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;">a</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"dedupe"</span><span class="o" style="font-weight: 600;">)){</span></span>
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<td class="old_line diff-line-num" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
125
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<td class="new_line diff-line-num" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
125
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC125" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//ignore</span></span>
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<td class="old_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
126
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC126" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span><span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</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;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"entryfilter"</span><span class="o" style="font-weight: 600;">)){</span></span>
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<td class="old_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
127
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC127" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//ignore</span></span>
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<td class="old_line diff-line-num" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
126
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<td class="new_line diff-line-num" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
128
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC128" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span><span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</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;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"markduplicates"</span><span class="o" style="font-weight: 600;">)){</span></span>
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<td class="old_line diff-line-num" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
127
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<td class="new_line diff-line-num" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
129
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC129" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//ignore</span></span>
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<td class="old_line diff-line-num" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
128
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<td class="new_line diff-line-num" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
130
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC130" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span><span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</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;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"markall"</span><span class="o" style="font-weight: 600;">)){</span></span>
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<li id="87e09ce245832e04b8a3d06edd667cfac9295e33">
<a href="https://salsa.debian.org/med-team/bbmap/-/commit/1c662261847da712e5b04b94277f8aa712c37619#87e09ce245832e04b8a3d06edd667cfac9295e33" style="color: #1068bf; text-decoration: none;"><strong style="font-weight: bold;">current/icecream/IceCreamFinder.java</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -76,6 +76,8 @@ public final class IceCreamFinder {</td>
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<td class="old_line diff-line-num" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
76
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76
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC76" class="line" lang="java"> <span class="n" style="color: #333;">outstream</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">pp</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">outstream</span><span class="o" style="font-weight: 600;">;</span></span>
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77
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <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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<td class="new_line diff-line-num" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
78
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC78" class="line" lang="java"> </span>
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<td class="old_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
79
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC79" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Parser</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setQuality</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">33</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
80
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC80" class="line" lang="java"> </span>
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<td class="old_line diff-line-num" 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: inherit;" align="right" bgcolor="#fafafa">
79
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<td class="new_line diff-line-num" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
81
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC81" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//Set shared static variables prior to parsing</span></span>
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<td class="old_line diff-line-num" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
80
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<td class="new_line diff-line-num" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
82
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC82" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">ReadWrite</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">USE_PIGZ</span><span class="o" style="font-weight: 600;">=</span><span class="nc" style="color: #458; font-weight: 600;">ReadWrite</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">USE_UNPIGZ</span><span class="o" style="font-weight: 600;">=</span><span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
81
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<td class="new_line diff-line-num" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
83
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC83" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">ReadWrite</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">USE_BGZIP</span><span class="o" style="font-weight: 600;">=</span><span class="nc" style="color: #458; font-weight: 600;">ReadWrite</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">USE_UNBGZIP</span><span class="o" style="font-weight: 600;">=</span><span class="nc" style="color: #458; font-weight: 600;">ReadWrite</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">PREFER_BGZIP</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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<a href="https://salsa.debian.org/med-team/bbmap/-/commit/1c662261847da712e5b04b94277f8aa712c37619#06a7eaaf098b8d2e7c18a48b5d98671b027f6af9" style="color: #1068bf; text-decoration: none;"><strong style="font-weight: bold;">current/jgi/BBDuk.java</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -321,9 +321,13 @@ public class BBDuk {</td>
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<td class="old_line diff-line-num" data-linenumber="321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
321
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<td class="new_line diff-line-num" data-linenumber="321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
321
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC321" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span><span class="o" style="font-weight: 600;">{</span><span class="n" style="color: #333;">ksplit_</span><span class="o" style="font-weight: 600;">=</span><span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;}</span></span>
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<td class="old_line diff-line-num" data-linenumber="322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
322
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<td class="new_line diff-line-num" data-linenumber="322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
322
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC322" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span><span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</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;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"ktrim"</span><span class="o" style="font-weight: 600;">)){</span></span>
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<td class="old_line diff-line-num" data-linenumber="323" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
323
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<td class="new_line diff-line-num" data-linenumber="323" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
323
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <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;">b</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;">b</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">""</span><span class="o" style="font-weight: 600;">;}</span></span>
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<td class="old_line diff-line-num old" data-linenumber="324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
324
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<td class="new_line diff-line-num old" data-linenumber="324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC324" 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;">b</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equalsIgnoreCase</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"left"</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equalsIgnoreCase</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"l"</span><span class="o" style="font-weight: 600;">)){</span><span class="n" style="color: #333;">ktrimLeft_</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 class="n" style="color: #333;">ktrimRight_</span><span class="o" style="font-weight: 600;">=</span><span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span><span class="n" style="color: #333;">ktrimN_</span><span class="o" style="font-weight: 600;">=</span><span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;}</span></span>
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<td class="old_line diff-line-num old" data-linenumber="325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
325
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<td class="new_line diff-line-num old" data-linenumber="324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC325" 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;">b</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equalsIgnoreCase</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"right"</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equalsIgnoreCase</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"r"</span><span class="o" style="font-weight: 600;">)){</span><span class="n" style="color: #333;">ktrimLeft_</span><span class="o" style="font-weight: 600;">=</span><span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span><span class="n" style="color: #333;">ktrimRight_</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 class="n" style="color: #333;">ktrimN_</span><span class="o" style="font-weight: 600;">=</span><span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;}</span></span>
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<td class="old_line diff-line-num old" data-linenumber="326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
326
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<td class="new_line diff-line-num old" data-linenumber="324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC326" 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;">b</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equalsIgnoreCase</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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324
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC324" 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;">b</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equalsIgnoreCase</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"rl"</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equalsIgnoreCase</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"lr"</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equalsIgnoreCase</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"tips"</span><span class="o" style="font-weight: 600;">)){</span></span>
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<td class="old_line diff-line-num new" data-linenumber="327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
325
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC325" class="line" lang="java"> <span class="n" style="color: #333;">ktrimLeft_</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ktrimRight_</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 class="n" style="color: #333;">ktrimN_</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ksplit_</span><span class="o" style="font-weight: 600;">=</span><span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
326
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC326" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span><span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equalsIgnoreCase</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"left"</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equalsIgnoreCase</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"l"</span><span class="o" style="font-weight: 600;">)){</span></span>
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<td class="old_line diff-line-num new" data-linenumber="327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
327
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC327" class="line" lang="java"> <span class="n" style="color: #333;">ktrimLeft_</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 class="n" style="color: #333;">ktrimRight_</span><span class="o" style="font-weight: 600;">=</span><span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span><span class="n" style="color: #333;">ktrimN_</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ksplit_</span><span class="o" style="font-weight: 600;">=</span><span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
328
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC328" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span><span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equalsIgnoreCase</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"right"</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equalsIgnoreCase</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"r"</span><span class="o" style="font-weight: 600;">)){</span></span>
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<td class="old_line diff-line-num new" data-linenumber="327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
329
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC329" class="line" lang="java"> <span class="n" style="color: #333;">ktrimLeft_</span><span class="o" style="font-weight: 600;">=</span><span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span><span class="n" style="color: #333;">ktrimRight_</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 class="n" style="color: #333;">ktrimN_</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ksplit_</span><span class="o" style="font-weight: 600;">=</span><span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
330
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC330" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span><span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equalsIgnoreCase</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="old_line diff-line-num" data-linenumber="327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
327
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<td class="new_line diff-line-num" data-linenumber="331" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
331
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC331" class="line" lang="java"> <span class="n" style="color: #333;">ktrimLeft_</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ktrimRight_</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ksplit_</span><span class="o" style="font-weight: 600;">=</span><span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
328
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<td class="new_line diff-line-num" data-linenumber="332" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
332
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC332" class="line" lang="java"> <span class="n" style="color: #333;">ktrimN_</span><span class="o" style="font-weight: 600;">=</span><span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
329
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<td class="new_line diff-line-num" data-linenumber="333" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
333
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC333" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span><span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">.</span><span class="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="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equalsIgnoreCase</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"t"</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equalsIgnoreCase</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"f"</span><span class="o" style="font-weight: 600;">)){</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="332" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="336" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -332,9 +336,15 @@ public class BBDuk {</td>
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<td class="old_line diff-line-num" data-linenumber="332" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
332
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<td class="new_line diff-line-num" data-linenumber="336" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
336
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC336" class="line" lang="java"> <span class="no" style="color: #008080;">TRIM_SYMBOL_</span><span class="o" style="font-weight: 600;">=(</span><span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="o" style="font-weight: 600;">)</span><span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">charAt</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="old_line diff-line-num" data-linenumber="333" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
333
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<td class="new_line diff-line-num" data-linenumber="337" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
337
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC337" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span><span class="k" style="font-weight: 600;">else</span><span class="o" style="font-weight: 600;">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="334" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
334
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<td class="new_line diff-line-num" data-linenumber="338" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
338
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC338" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">!=</span><span class="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;">b</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equalsIgnoreCase</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"f"</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equalsIgnoreCase</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"false"</span><span class="o" style="font-weight: 600;">)))</span> <span class="o" style="font-weight: 600;">:</span></span>
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335
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<td class="new_line diff-line-num old" data-linenumber="339" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC335" class="line" lang="java"> <span class="s" style="color: #d14;">"\nInvalid setting for ktrim - values must be f (false), l (left), r (right), or n."</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="336" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="339" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
339
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC339" class="line" lang="java"> <span class="s" style="color: #d14;">"\nInvalid setting for ktrim - values must be f (false), l (left), r (right), <span class="idiff left right addition" style="background-color: #c7f0d2;">rl (tips), </span>or n."</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="336" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
336
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<td class="new_line diff-line-num" data-linenumber="340" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
340
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC340" class="line" lang="java"> <span class="n" style="color: #333;">ktrimRight_</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ktrimLeft_</span><span class="o" style="font-weight: 600;">=</span><span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="337" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
337
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<td class="new_line diff-line-num" data-linenumber="341" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
341
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC341" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="old_line diff-line-num new" data-linenumber="338" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="342" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
342
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC342" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span><span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</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;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"trimtips"</span><span class="o" style="font-weight: 600;">)</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;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"ktrimtips"</span><span class="o" style="font-weight: 600;">)){</span></span>
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<td class="old_line diff-line-num new" data-linenumber="338" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="343" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
343
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC343" 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;">b</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;">b</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">""</span><span class="o" style="font-weight: 600;">;}</span></span>
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<td class="old_line diff-line-num new" data-linenumber="338" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="344" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
344
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC344" 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;">b</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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<td class="old_line diff-line-num new" data-linenumber="338" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="345" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
345
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC345" class="line" lang="java"> <span class="n" style="color: #333;">ktrimLeft_</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ktrimRight_</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 class="n" style="color: #333;">ktrimN_</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ksplit_</span><span class="o" style="font-weight: 600;">=</span><span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="338" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="346" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
346
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC346" class="line" lang="java"> <span class="n" style="color: #333;">restrictLeft_</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">restrictRight_</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;">b</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="338" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="347" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
347
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC347" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="338" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
338
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<td class="new_line diff-line-num" data-linenumber="348" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
348
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC348" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span><span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</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;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"kmask"</span><span class="o" style="font-weight: 600;">)</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;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"mask"</span><span class="o" style="font-weight: 600;">)){</span></span>
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<td class="old_line diff-line-num" data-linenumber="339" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
339
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<td class="new_line diff-line-num" data-linenumber="349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
349
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC349" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"lc"</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equalsIgnoreCase</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="s" style="color: #d14;">"lowercase"</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equalsIgnoreCase</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">)){</span></span>
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<td class="old_line diff-line-num" data-linenumber="340" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
340
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<td class="new_line diff-line-num" data-linenumber="350" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
350
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC350" class="line" lang="java"> <span class="n" style="color: #333;">kmaskLowercase_</span><span class="o" style="font-weight: 600;">=</span><span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2454" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2464" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -2454,7 +2464,8 @@ public class BBDuk {</td>
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<td class="old_line diff-line-num" data-linenumber="2454" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
2454
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<td class="new_line diff-line-num" data-linenumber="2464" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
2464
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2464" class="line" lang="java"> <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;">Read</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">bad</span><span class="o" style="font-weight: 600;">=(</span><span class="n" style="color: #333;">rosb</span><span class="o" style="font-weight: 600;">==</span><span class="kc" style="font-weight: 600;">null</span> <span class="o" style="font-weight: 600;">?</span> <span class="kc" style="font-weight: 600;">null</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;">Read</span><span class="o" style="font-weight: 600;">>(</span><span class="nc" style="color: #458; font-weight: 600;">Shared</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">bufferLen</span><span class="o" style="font-weight: 600;">()));</span></span>
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2455
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<td class="new_line diff-line-num" data-linenumber="2465" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
2465
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2465" class="line" lang="java"> <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;">Read</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">single</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;">Read</span><span class="o" style="font-weight: 600;">>(</span><span class="nc" style="color: #458; font-weight: 600;">Shared</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">bufferLen</span><span class="o" style="font-weight: 600;">());</span></span>
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<td class="old_line diff-line-num" data-linenumber="2456" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
2456
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<td class="new_line diff-line-num" data-linenumber="2466" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
2466
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2466" class="line" lang="java"> </span>
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<td class="old_line diff-line-num old" data-linenumber="2457" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
2457
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<td class="new_line diff-line-num old" data-linenumber="2467" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC2457" class="line" lang="java"> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">ktrimrl</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ktrimLeft</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">ktrimRight</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2458" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2467" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2467
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC2467" class="line" lang="java"> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">ktrimLeftOrRight</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ktrimLeft</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">ktrimRight</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2458" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2468" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2468
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC2468" class="line" lang="java"> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">ktrimTips</span><span class="o" style="font-weight: 600;">=(</span><span class="n" style="color: #333;">ktrimLeft</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">ktrimRight</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="2458" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
2458
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<td class="new_line diff-line-num" data-linenumber="2469" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
2469
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2469" class="line" lang="java"> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">doKmerTrimming</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">storedKmers</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;">ktrimLeft</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">ktrimRight</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">ktrimN</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">ksplit</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="2459" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
2459
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<td class="new_line diff-line-num" data-linenumber="2470" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
2470
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2470" class="line" lang="java"> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">doKmerFiltering</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">storedKmers</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;">doKmerTrimming</span><span class="o" style="font-weight: 600;">;</span></span>
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2460
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<td class="new_line diff-line-num" data-linenumber="2471" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
2471
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2471" class="line" lang="java"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2641" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2652" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -2641,7 +2652,22 @@ public class BBDuk {</td>
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<td class="old_line diff-line-num" data-linenumber="2641" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
2641
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<td class="new_line diff-line-num" data-linenumber="2652" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
2652
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2652" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">xsum</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="old_line diff-line-num" data-linenumber="2642" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
2642
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<td class="new_line diff-line-num" data-linenumber="2653" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
2653
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2653" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">rktsum</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="old_line diff-line-num" data-linenumber="2643" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
2643
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<td class="new_line diff-line-num" data-linenumber="2654" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
2654
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2654" class="line" lang="java"> </span>
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<td class="old_line diff-line-num old" data-linenumber="2644" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
2644
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<td class="new_line diff-line-num old" data-linenumber="2655" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC2644" 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;">ktrimrl</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2655" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2655
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC2655" 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;">ktrimTips</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2656" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2656
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC2656" 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;">r1</span><span class="o" style="font-weight: 600;">!=</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2657" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2657
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC2657" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ktrimTips</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">r1</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">keySets</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2658" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2658
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC2658" class="line" lang="java"> <span class="n" style="color: #333;">xsum</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2659" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2659
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC2659" class="line" lang="java"> <span class="n" style="color: #333;">rktsum</span><span class="o" style="font-weight: 600;">+=(</span><span class="n" style="color: #333;">x</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="mi" style="color: #099;">1</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="old_line diff-line-num new" data-linenumber="2645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2660" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2660
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC2660" class="line" lang="java"> <span class="n" style="color: #333;">rlen1</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">r1</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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<td class="old_line diff-line-num new" data-linenumber="2645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2661
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC2661" 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;">rlen1</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">minlen1</span><span class="o" style="font-weight: 600;">){</span><span class="n" style="color: #333;">setDiscarded</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">r1</span><span class="o" style="font-weight: 600;">);}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2662
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC2662" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2663" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2663
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC2663" 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;">r2</span><span class="o" style="font-weight: 600;">!=</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2664" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2664
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC2664" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ktrimTips</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">r2</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">keySets</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2665" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2665
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC2665" class="line" lang="java"> <span class="n" style="color: #333;">xsum</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2666" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2666
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC2666" class="line" lang="java"> <span class="n" style="color: #333;">rktsum</span><span class="o" style="font-weight: 600;">+=(</span><span class="n" style="color: #333;">x</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="mi" style="color: #099;">1</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="old_line diff-line-num new" data-linenumber="2645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2667" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2667
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC2667" class="line" lang="java"> <span class="n" style="color: #333;">rlen2</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">r2</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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<td class="old_line diff-line-num new" data-linenumber="2645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2668" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2668
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC2668" 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;">rlen2</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">minlen2</span><span class="o" style="font-weight: 600;">){</span><span class="n" style="color: #333;">setDiscarded</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">r2</span><span class="o" style="font-weight: 600;">);}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2669" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2669
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC2669" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2670" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2670
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC2670" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span><span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ktrimLeftOrRight</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="old_line diff-line-num" data-linenumber="2645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
2645
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<td class="new_line diff-line-num" data-linenumber="2671" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
2671
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2671" 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;">r1</span><span class="o" style="font-weight: 600;">!=</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="old_line diff-line-num" data-linenumber="2646" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
2646
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<td class="new_line diff-line-num" data-linenumber="2672" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
2672
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2672" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ktrim</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">r1</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">keySets</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="2647" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
2647
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<td class="new_line diff-line-num" data-linenumber="2673" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
2673
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2673" class="line" lang="java"> <span class="n" style="color: #333;">xsum</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">x</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="3555" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3581" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -3555,13 +3581,195 @@ public class BBDuk {</td>
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3555
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<td class="new_line diff-line-num" data-linenumber="3581" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
3581
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC3581" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">found</span><span class="o" style="font-weight: 600;">;</span></span>
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3556
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3582
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC3582" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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3557
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3583
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC3583" class="line" lang="java"> </span>
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<td class="new_line diff-line-num new" data-linenumber="3584" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3584
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3584" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">ktrim</span><span class="o" style="font-weight: 600;">(</span><span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">Read</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">,</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">AbstractKmerTable</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">sets</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3585" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3585
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3585" class="line" lang="java"> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">len</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="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">();</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3586" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3586
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3586" class="line" lang="java"> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">start</span><span class="o" style="font-weight: 600;">=(</span><span class="n" style="color: #333;">restrictRight</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="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">:</span> <span class="nc" style="color: #458; font-weight: 600;">Tools</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">max</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">len</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">restrictRight</span><span class="o" style="font-weight: 600;">));</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3587" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3587
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3587" class="line" lang="java"> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">stop</span><span class="o" style="font-weight: 600;">=(</span><span class="n" style="color: #333;">restrictLeft</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;">len</span> <span class="o" style="font-weight: 600;">:</span> <span class="nc" style="color: #458; font-weight: 600;">Tools</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">min</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">len</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">restrictLeft</span><span class="o" style="font-weight: 600;">));</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3588" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3588
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3588" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="nf" style="color: #900; font-weight: 600;">ktrim</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;">sets</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">start</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">stop</span><span class="o" style="font-weight: 600;">);</span></span>
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3589
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3589" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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3590
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3590" class="line" lang="java"> </span>
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<td class="new_line diff-line-num new" data-linenumber="3591" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3591
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3591" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">ktrimTips</span><span class="o" style="font-weight: 600;">(</span><span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">Read</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">,</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">AbstractKmerTable</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">sets</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3592" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3592
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3592" class="line" lang="java"> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">len</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="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">();</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3593" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3593
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3593" class="line" lang="java"> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mid</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">len</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;">k</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="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3594" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3594
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3594" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sum</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="new_line diff-line-num new" data-linenumber="3595" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3595
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3595" 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;">ktrimRight</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3596" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3596
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3596" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">start</span><span class="o" style="font-weight: 600;">=</span><span class="nc" style="color: #458; font-weight: 600;">Tools</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">max</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">,</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">restrictRight</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;">mid</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">len</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">restrictRight</span><span class="o" style="font-weight: 600;">));</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3597" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3597
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3597" class="line" lang="java"> <span class="n" style="color: #333;">sum</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">ktrimTip</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;">sets</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">start</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">len</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 class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3598
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3598" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3599" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3599
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3599" 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;">ktrimLeft</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3600" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3600
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3600" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">stop</span><span class="o" style="font-weight: 600;">=</span><span class="nc" style="color: #458; font-weight: 600;">Tools</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">min</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="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;">restrictLeft</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;">mid</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">restrictLeft</span><span class="o" style="font-weight: 600;">));</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3601" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3601
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3601" class="line" lang="java"> <span class="n" style="color: #333;">sum</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">ktrimTip</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;">sets</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;">stop</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3602" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3602
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3602" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3603" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3603
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3603" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">sum</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3604" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3604
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3604" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3605" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3605
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3605" class="line" lang="java"> </span>
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<td class="new_line diff-line-num new" data-linenumber="3606" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3606
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3606" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<td class="old_line diff-line-num new" data-linenumber="3558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="3607" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3607
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3607" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Trim a read to remove matching kmers and everything to their left or right, on one end.</span></span>
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<td class="old_line diff-line-num new" data-linenumber="3558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="3608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3608
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3608" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Allows both trimRight and trimLeft, in 2 passes.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3609" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3609
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3609" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @param r Read to process</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3610" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3610
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3610" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @param sets Kmer tables</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3611" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3611
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3611" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @return Number of bases trimmed</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3612" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3612
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3612" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<td class="old_line diff-line-num new" data-linenumber="3558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="3613" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3613
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3613" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">ktrimTip</span><span class="o" style="font-weight: 600;">(</span><span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">Read</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">,</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">AbstractKmerTable</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">sets</span><span class="o" style="font-weight: 600;">,</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">start</span><span class="o" style="font-weight: 600;">,</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">stop</span><span class="o" style="font-weight: 600;">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="3558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="3614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3614
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3614" class="line" lang="java"> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">right</span><span class="o" style="font-weight: 600;">,</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">left</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3615" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3615
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3615" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">left</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">right</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="3558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="3616" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3616
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3616" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(!(</span><span class="n" style="color: #333;">left</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">right</span><span class="o" style="font-weight: 600;">));</span></span>
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<td class="old_line diff-line-num new" data-linenumber="3558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="3617" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3617
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3617" 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;">r</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;">r</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="nc" style="color: #458; font-weight: 600;">Tools</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">max</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;">useShortKmers</span> <span class="o" style="font-weight: 600;">?</span> <span class="nc" style="color: #458; font-weight: 600;">Tools</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">min</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">mink</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">storedKmers</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">){</span><span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;}</span></span>
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<td class="old_line diff-line-num new" data-linenumber="3558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="3618" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3618
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3618" 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;">skipR1</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="na" style="color: #008080;">pairnum</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="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">skipR2</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="na" style="color: #008080;">pairnum</span><span class="o" style="font-weight: 600;">()==</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)){</span><span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3619
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3619" 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;">verbose</span><span class="o" style="font-weight: 600;">){</span><span class="n" style="color: #333;">outstream</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;">"KTrimming read "</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="na" style="color: #008080;">id</span><span class="o" style="font-weight: 600;">);}</span></span>
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<td class="old_line diff-line-num new" data-linenumber="3558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="3620" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3620
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3620" class="line" lang="java"> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">bases</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">bases</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">quals</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="na" style="color: #008080;">quality</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="3558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="3621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3621
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3621" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">kmer</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="new_line diff-line-num new" data-linenumber="3622" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3622
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3622" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">rkmer</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="new_line diff-line-num new" data-linenumber="3623" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3623
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3623" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">found</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="new_line diff-line-num new" data-linenumber="3624" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3624
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3624" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">len</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3625" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3625
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3625" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">id0</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="c1" style="color: #998; font-style: italic;">//ID of first kmer found.</span></span>
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<td class="old_line diff-line-num new" data-linenumber="3558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="3626" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3626
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3626" class="line" lang="java"> </span>
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<td class="old_line diff-line-num new" data-linenumber="3558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="3627" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3627
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3627" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minLoc</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">999999999</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">minLocExclusive</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">999999999</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3628" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3628
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3628" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxLoc</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;">maxLocExclusive</span><span class="o" style="font-weight: 600;">=-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3629
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3629" class="line" lang="java"> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">initialLength</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="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">();</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3630" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3630
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3630" class="line" lang="java"> </span>
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<td class="old_line diff-line-num new" data-linenumber="3558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="3631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3631
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3631" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//Scan for normal kmers</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3632
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3632" 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;">start</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;">stop</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3633" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3633
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3633" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">byte</span> <span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">bases</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">];</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3634" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3634
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3634" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">symbolToNumber0</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">];</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3635" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3635
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3635" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">x2</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">symbolToComplementNumber0</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">];</span></span>
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<td class="old_line diff-line-num new" data-linenumber="3558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="3636" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3636
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3636" class="line" lang="java"> <span class="n" style="color: #333;">kmer</span><span class="o" style="font-weight: 600;">=((</span><span class="n" style="color: #333;">kmer</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">bitsPerBase</span><span class="o" style="font-weight: 600;">)|</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">)&</span><span class="n" style="color: #333;">mask</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="3558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="3637" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3637
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3637" class="line" lang="java"> <span class="n" style="color: #333;">rkmer</span><span class="o" style="font-weight: 600;">=((</span><span class="n" style="color: #333;">rkmer</span><span class="o" style="font-weight: 600;">>>></span><span class="n" style="color: #333;">bitsPerBase</span><span class="o" style="font-weight: 600;">)|(</span><span class="n" style="color: #333;">x2</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">shift2</span><span class="o" style="font-weight: 600;">))&</span><span class="n" style="color: #333;">mask</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="3558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="3638" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3638
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3638" 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;">forbidNs</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">isFullyDefined</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">)){</span><span class="n" style="color: #333;">len</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;">rkmer</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;">else</span><span class="o" style="font-weight: 600;">{</span><span class="n" style="color: #333;">len</span><span class="o" style="font-weight: 600;">++;}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3639
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3639" 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;">verbose</span><span class="o" style="font-weight: 600;">){</span><span class="n" style="color: #333;">outstream</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;">"Scanning3 i="</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">", kmer="</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">kmer</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">", rkmer="</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">rkmer</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">", len="</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">len</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">", bases="</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;">bases</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">Tools</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">max</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">k2</span><span class="o" style="font-weight: 600;">),</span> <span class="nc" style="color: #458; font-weight: 600;">Tools</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">min</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;">k</span><span class="o" style="font-weight: 600;">)));}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3640" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3640
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3640" 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;">len</span><span class="o" style="font-weight: 600;">>=</span><span class="n" style="color: #333;">minlen2</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;">minlen</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3641" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3641
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3641" class="line" lang="java"> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">id</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">getValue</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">kmer</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">rkmer</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">kmask</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;">k</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">qHammingDistance</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">sets</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3642" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3642
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3642" 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;">id</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="new_line diff-line-num new" data-linenumber="3643" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3643
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3643" 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;">id0</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;">id0</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">id</span><span class="o" style="font-weight: 600;">;}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3644" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3644
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3644" class="line" lang="java"> <span class="n" style="color: #333;">minLoc</span><span class="o" style="font-weight: 600;">=</span><span class="nc" style="color: #458; font-weight: 600;">Tools</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">min</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">minLoc</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;">k</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3645
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3645" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">minLoc</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="new_line diff-line-num new" data-linenumber="3646" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3646
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3646" class="line" lang="java"> <span class="n" style="color: #333;">maxLoc</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3647" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3647
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3647" class="line" lang="java"> <span class="n" style="color: #333;">found</span><span class="o" style="font-weight: 600;">++;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3648" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3648
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3648" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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3649
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3649" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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3650
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3650" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3651" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3651
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3651" class="line" lang="java"> </span>
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<td class="new_line diff-line-num new" data-linenumber="3652" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3652
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3652" 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;">minLoc</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">minLocExclusive</span><span class="o" style="font-weight: 600;">){</span><span class="n" style="color: #333;">minLocExclusive</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">minLoc</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">;}</span></span>
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3653
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3653" 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;">maxLoc</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">maxLocExclusive</span><span class="o" style="font-weight: 600;">){</span><span class="n" style="color: #333;">maxLocExclusive</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">maxLoc</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">;}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3654" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3654
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3654" class="line" lang="java"> </span>
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<td class="old_line diff-line-num new" data-linenumber="3558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="3655" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3655
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3655" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//If nothing was found, scan for short kmers. Only used for trimming.</span></span>
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<td class="old_line diff-line-num new" data-linenumber="3558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="3656" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3656
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3656" 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;">useShortKmers</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">found</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="new_line diff-line-num new" data-linenumber="3657" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3657
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3657" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">maskMiddle</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">middleMask</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;">maskMiddle</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;">middleMask</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">", k="</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">", mink="</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">mink</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3658" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3658
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3658" class="line" lang="java"> </span>
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<td class="old_line diff-line-num new" data-linenumber="3558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="3659" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3659
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3659" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//Look for short kmers on left side</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3660" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3660
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3660" 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;">left</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3661
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3661" class="line" lang="java"> <span class="n" style="color: #333;">kmer</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="new_line diff-line-num new" data-linenumber="3662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3662
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3662" class="line" lang="java"> <span class="n" style="color: #333;">rkmer</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="new_line diff-line-num new" data-linenumber="3663" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3663
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3663" class="line" lang="java"> <span class="n" style="color: #333;">len</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3664" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3664
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3664" class="line" lang="java"> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">lim</span><span class="o" style="font-weight: 600;">=</span><span class="nc" style="color: #458; font-weight: 600;">Tools</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">min</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">stop</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3665" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3665
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3665" 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;">start</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;">lim</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3666" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3666
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3666" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">byte</span> <span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">bases</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">];</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3667" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3667
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3667" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">symbolToNumber0</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">];</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3668" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3668
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3668" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">x2</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">symbolToComplementNumber0</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">];</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3669" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3669
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3669" class="line" lang="java"> <span class="n" style="color: #333;">kmer</span><span class="o" style="font-weight: 600;">=((</span><span class="n" style="color: #333;">kmer</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">bitsPerBase</span><span class="o" style="font-weight: 600;">)|</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">)&</span><span class="n" style="color: #333;">mask</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3670" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3670
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3670" class="line" lang="java"> <span class="n" style="color: #333;">rkmer</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">rkmer</span><span class="o" style="font-weight: 600;">|(</span><span class="n" style="color: #333;">x2</span><span class="o" style="font-weight: 600;"><<(</span><span class="n" style="color: #333;">bitsPerBase</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">len</span><span class="o" style="font-weight: 600;">));</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3671" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3671
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3671" class="line" lang="java"> <span class="n" style="color: #333;">len</span><span class="o" style="font-weight: 600;">++;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3672" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3672
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3672" 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;">verbose</span><span class="o" style="font-weight: 600;">){</span><span class="n" style="color: #333;">outstream</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;">"Scanning4 i="</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">", kmer="</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">kmer</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">", rkmer="</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">rkmer</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">", bases="</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;">bases</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">Tools</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">max</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">k2</span><span class="o" style="font-weight: 600;">),</span> <span class="nc" style="color: #458; font-weight: 600;">Tools</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">min</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;">k</span><span class="o" style="font-weight: 600;">)));}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3673" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3673
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3673" 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;">len</span><span class="o" style="font-weight: 600;">>=</span><span class="n" style="color: #333;">mink</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3674" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3674
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3674" class="line" lang="java"> </span>
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<td class="new_line diff-line-num new" data-linenumber="3675" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3675
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3675" 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;">verbose</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3676" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3676
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3676" class="line" lang="java"> <span class="n" style="color: #333;">outstream</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 for left kmer "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">kmerToString</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">kmer</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">len</span><span class="o" style="font-weight: 600;">));</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3677" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3677
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3677" class="line" lang="java"> <span class="n" style="color: #333;">outstream</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 for left rkmer "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">kmerToString</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">rkmer</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">len</span><span class="o" style="font-weight: 600;">));</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3678" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3678
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3678" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3679" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3679
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3679" class="line" lang="java"> </span>
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<td class="old_line diff-line-num new" data-linenumber="3558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="3680" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3680
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3680" class="line" lang="java"> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">id</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">getValue</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">kmer</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">rkmer</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">lengthMasks</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">len</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;">len</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">qHammingDistance2</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">sets</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3681" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3681
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3681" 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;">id</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="new_line diff-line-num new" data-linenumber="3682" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3682
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3682" 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;">id0</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;">id0</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">id</span><span class="o" style="font-weight: 600;">;}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3683" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3683
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3683" 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;">verbose</span><span class="o" style="font-weight: 600;">){</span><span class="n" style="color: #333;">outstream</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;">"Found "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">kmer</span><span class="o" style="font-weight: 600;">);}</span></span>
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<td class="old_line diff-line-num new" data-linenumber="3558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="3684" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3684
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3684" class="line" lang="java"> <span class="n" style="color: #333;">minLoc</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="new_line diff-line-num new" data-linenumber="3685" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3685
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3685" class="line" lang="java"> <span class="n" style="color: #333;">minLocExclusive</span><span class="o" style="font-weight: 600;">=</span><span class="nc" style="color: #458; font-weight: 600;">Tools</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">min</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">minLocExclusive</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>
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<td class="new_line diff-line-num new" data-linenumber="3686" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3686
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3686" class="line" lang="java"> <span class="n" style="color: #333;">maxLoc</span><span class="o" style="font-weight: 600;">=</span><span class="nc" style="color: #458; font-weight: 600;">Tools</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">max</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">maxLoc</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3687" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3687
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3687" class="line" lang="java"> <span class="n" style="color: #333;">maxLocExclusive</span><span class="o" style="font-weight: 600;">=</span><span class="nc" style="color: #458; font-weight: 600;">Tools</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">max</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">maxLocExclusive</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="new_line diff-line-num new" data-linenumber="3688" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3688
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3688" class="line" lang="java"> <span class="n" style="color: #333;">found</span><span class="o" style="font-weight: 600;">++;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3689" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3689
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3689" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3690" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3690
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3690" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3691" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3691
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3691" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3692" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3692
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3692" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3693" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3693
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3693" class="line" lang="java"></span>
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<td class="new_line diff-line-num new" data-linenumber="3694" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3694
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3694" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//Look for short kmers on right side</span></span>
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<td class="old_line diff-line-num new" data-linenumber="3558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="3695" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3695
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3695" 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;">right</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3696" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3696
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3696" class="line" lang="java"> <span class="n" style="color: #333;">kmer</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="new_line diff-line-num new" data-linenumber="3697" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3697
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3697" class="line" lang="java"> <span class="n" style="color: #333;">rkmer</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="new_line diff-line-num new" data-linenumber="3698" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3698
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3698" class="line" lang="java"> <span class="n" style="color: #333;">len</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3699" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3699
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3699" class="line" lang="java"> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">lim</span><span class="o" style="font-weight: 600;">=</span><span class="nc" style="color: #458; font-weight: 600;">Tools</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">max</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;">stop</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3700" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3700
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3700" 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;">stop</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;">lim</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">--){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3701" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3701
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3701" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">byte</span> <span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">bases</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">];</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3702" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3702
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3702" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">symbolToNumber0</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">];</span></span>
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<td class="old_line diff-line-num new" data-linenumber="3558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="3703" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3703
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3703" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">x2</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">symbolToComplementNumber0</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">];</span></span>
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<td class="old_line diff-line-num new" data-linenumber="3558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="3704" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3704
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3704" class="line" lang="java"> <span class="n" style="color: #333;">kmer</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">kmer</span><span class="o" style="font-weight: 600;">|(</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;"><<(</span><span class="n" style="color: #333;">bitsPerBase</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">len</span><span class="o" style="font-weight: 600;">));</span></span>
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<td class="old_line diff-line-num new" data-linenumber="3558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="3705" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3705
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3705" class="line" lang="java"> <span class="n" style="color: #333;">rkmer</span><span class="o" style="font-weight: 600;">=((</span><span class="n" style="color: #333;">rkmer</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">bitsPerBase</span><span class="o" style="font-weight: 600;">)|</span><span class="n" style="color: #333;">x2</span><span class="o" style="font-weight: 600;">)&</span><span class="n" style="color: #333;">mask</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3706" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3706
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3706" class="line" lang="java"> <span class="n" style="color: #333;">len</span><span class="o" style="font-weight: 600;">++;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="3558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="3707" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3707
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3707" 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;">verbose</span><span class="o" style="font-weight: 600;">){</span><span class="n" style="color: #333;">outstream</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;">"Scanning5 i="</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">", kmer="</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">kmer</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">", rkmer="</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">rkmer</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">", bases="</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;">bases</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">Tools</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">max</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">k2</span><span class="o" style="font-weight: 600;">),</span> <span class="nc" style="color: #458; font-weight: 600;">Tools</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">min</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;">k</span><span class="o" style="font-weight: 600;">)));}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3708" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3708
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3708" 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;">len</span><span class="o" style="font-weight: 600;">>=</span><span class="n" style="color: #333;">mink</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3709" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3709
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3709" 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;">verbose</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3710" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3710
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3710" class="line" lang="java"> <span class="n" style="color: #333;">outstream</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 for right kmer "</span><span class="o" style="font-weight: 600;">+</span></span>
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<td class="old_line diff-line-num new" data-linenumber="3558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="3711" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3711
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3711" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">AminoAcid</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">kmerToString</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">kmer</span><span class="o" style="font-weight: 600;">&~</span><span class="n" style="color: #333;">lengthMasks</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">len</span><span class="o" style="font-weight: 600;">],</span> <span class="n" style="color: #333;">len</span><span class="o" style="font-weight: 600;">)+</span><span class="s" style="color: #d14;">"; value="</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">toValue</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">kmer</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">rkmer</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">lengthMasks</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">len</span><span class="o" style="font-weight: 600;">])+</span><span class="s" style="color: #d14;">"; kmask="</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">lengthMasks</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">len</span><span class="o" style="font-weight: 600;">]);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3712" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3712
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3712" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3713" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3713
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3713" class="line" lang="java"> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">id</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">getValue</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">kmer</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">rkmer</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">lengthMasks</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">len</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;">len</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">qHammingDistance2</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">sets</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3714
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3714" 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;">id</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="new_line diff-line-num new" data-linenumber="3715" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3715
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3715" 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;">id0</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;">id0</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">id</span><span class="o" style="font-weight: 600;">;}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3716" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3716
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3716" 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;">verbose</span><span class="o" style="font-weight: 600;">){</span><span class="n" style="color: #333;">outstream</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;">"Found "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">kmer</span><span class="o" style="font-weight: 600;">);}</span></span>
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<td class="old_line diff-line-num new" data-linenumber="3558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="3717" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3717
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3717" class="line" lang="java"> <span class="n" style="color: #333;">minLoc</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3718
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3718" class="line" lang="java"> <span class="n" style="color: #333;">minLocExclusive</span><span class="o" style="font-weight: 600;">=</span><span class="nc" style="color: #458; font-weight: 600;">Tools</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">min</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">minLocExclusive</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">bases</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3719
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3719" class="line" lang="java"> <span class="n" style="color: #333;">maxLoc</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">bases</span><span class="o" style="font-weight: 600;">.</span><span class="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>
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<td class="new_line diff-line-num new" data-linenumber="3720" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3720
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3720" class="line" lang="java"> <span class="n" style="color: #333;">maxLocExclusive</span><span class="o" style="font-weight: 600;">=</span><span class="nc" style="color: #458; font-weight: 600;">Tools</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">max</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">maxLocExclusive</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>
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<td class="new_line diff-line-num new" data-linenumber="3721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3721
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3721" class="line" lang="java"> <span class="n" style="color: #333;">found</span><span class="o" style="font-weight: 600;">++;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3722" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3722
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3722" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3723
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3723" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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3724
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3724" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3725" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3725
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3725" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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3726
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3726" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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3727
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3727" class="line" lang="java"> </span>
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3728
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3728" class="line" lang="java"> </span>
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<td class="new_line diff-line-num new" data-linenumber="3729" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3729
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3729" 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;">verbose</span><span class="o" style="font-weight: 600;">){</span><span class="n" style="color: #333;">outstream</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;">"found="</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">found</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">", minLoc="</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">minLoc</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">", maxLoc="</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">maxLoc</span><span class="o" style="font-weight: 600;">+</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3730" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3730
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3730" class="line" lang="java"> <span class="s" style="color: #d14;">", minLocExclusive="</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">minLocExclusive</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">", maxLocExclusive="</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">maxLocExclusive</span><span class="o" style="font-weight: 600;">);}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3731" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3731
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3731" class="line" lang="java"> </span>
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<td class="new_line diff-line-num new" data-linenumber="3732" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3732
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3732" 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;">found</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="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3733" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3733
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3733" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">found</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="s" style="color: #d14;">"Overflow in 'found' variable."</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3734" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3734
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3734" class="line" lang="java"> </span>
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<td class="new_line diff-line-num new" data-linenumber="3735" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3735
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3735" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span><span class="c1" style="color: #998; font-style: italic;">//Increment counter for the scaffold whose kmer was first detected</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3736" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3736
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3736" 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;">scaffoldReadCountsT</span><span class="o" style="font-weight: 600;">!=</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3737" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3737
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3737" class="line" lang="java"> <span class="n" style="color: #333;">scaffoldReadCountsT</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">id0</span><span class="o" style="font-weight: 600;">]++;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3738" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3738
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3738" class="line" lang="java"> <span class="n" style="color: #333;">scaffoldBaseCountsT</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">id0</span><span class="o" style="font-weight: 600;">]+=</span><span class="n" style="color: #333;">bases</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3739
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3739" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span><span class="k" style="font-weight: 600;">else</span><span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3740" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3740
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3740" class="line" lang="java"> <span class="n" style="color: #333;">scaffoldReadCounts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addAndGet</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">id0</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3741" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3741
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3741" class="line" lang="java"> <span class="n" style="color: #333;">scaffoldBaseCounts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addAndGet</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">id0</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">bases</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">);</span></span>
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3742
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3742" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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3743
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3743" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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3744
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3744" class="line" lang="java"> </span>
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3745
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3745" 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;">trimPad</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="new_line diff-line-num new" data-linenumber="3746" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3746
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3746" class="line" lang="java"> <span class="n" style="color: #333;">maxLoc</span><span class="o" style="font-weight: 600;">=</span><span class="nc" style="color: #458; font-weight: 600;">Tools</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">mid</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;">maxLoc</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">trimPad</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">bases</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3747" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3747
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3747" class="line" lang="java"> <span class="n" style="color: #333;">minLoc</span><span class="o" style="font-weight: 600;">=</span><span class="nc" style="color: #458; font-weight: 600;">Tools</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">mid</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;">minLoc</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">trimPad</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">bases</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3748
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3748" class="line" lang="java"> <span class="n" style="color: #333;">maxLocExclusive</span><span class="o" style="font-weight: 600;">=</span><span class="nc" style="color: #458; font-weight: 600;">Tools</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">mid</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;">maxLocExclusive</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">trimPad</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">bases</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3749" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3749
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3749" class="line" lang="java"> <span class="n" style="color: #333;">minLocExclusive</span><span class="o" style="font-weight: 600;">=</span><span class="nc" style="color: #458; font-weight: 600;">Tools</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">mid</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;">minLocExclusive</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">trimPad</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">bases</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3750" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3750
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3750" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3751" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3751
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3751" class="line" lang="java"> </span>
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<td class="old_line diff-line-num new" data-linenumber="3558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="3752" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3752
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3752" 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;">left</span><span class="o" style="font-weight: 600;">){</span> <span class="c1" style="color: #998; font-style: italic;">//Trim from the read start to the rightmost kmer base</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3753" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3753
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3753" 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;">verbose</span><span class="o" style="font-weight: 600;">){</span><span class="n" style="color: #333;">outstream</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;">"Left trimming to "</span><span class="o" style="font-weight: 600;">+(</span><span class="n" style="color: #333;">ktrimExclusive</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">maxLocExclusive</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;">maxLoc</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="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">);}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3754" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3754
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3754" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">=</span><span class="nc" style="color: #458; font-weight: 600;">TrimRead</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">trimToPosition</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;">ktrimExclusive</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">maxLocExclusive</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;">maxLoc</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;">bases</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="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3755" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3755
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3755" 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;">verbose</span><span class="o" style="font-weight: 600;">){</span><span class="n" style="color: #333;">outstream</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;">"Trimmed "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" bases: "</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;">r</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">bases</span><span class="o" style="font-weight: 600;">));}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3756" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3756
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3756" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="3558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="3757" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3757
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3757" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span><span class="k" style="font-weight: 600;">else</span><span class="o" style="font-weight: 600;">{</span> <span class="c1" style="color: #998; font-style: italic;">//Trim from the leftmost kmer base to the read stop</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3758" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3758
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3758" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">right</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3759" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3759
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3759" 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;">verbose</span><span class="o" style="font-weight: 600;">){</span><span class="n" style="color: #333;">outstream</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;">"Right trimming to "</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;">ktrimExclusive</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">minLocExclusive</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;">minLoc</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">));}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3760" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3760
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3760" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">=</span><span class="nc" style="color: #458; font-weight: 600;">TrimRead</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">trimToPosition</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="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">ktrimExclusive</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">minLocExclusive</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;">minLoc</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="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3761" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3761
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3761" 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;">verbose</span><span class="o" style="font-weight: 600;">){</span><span class="n" style="color: #333;">outstream</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;">"Trimmed "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" bases: "</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;">r</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">bases</span><span class="o" style="font-weight: 600;">));}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3762" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3762
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3762" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">;</span></span>
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3763
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3763" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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3764
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3764" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3765" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3765
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3765" class="line" lang="java"> </span>
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3558
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<td class="new_line diff-line-num" data-linenumber="3766" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
3766
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC3766" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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3559
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<td class="new_line diff-line-num" data-linenumber="3767" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
3767
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC3767" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Trim a read to remove matching kmers and everything to their left or right.</span></span>
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3560
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<td class="new_line diff-line-num" data-linenumber="3768" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
3768
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC3768" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @param r Read to process</span></span>
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3561
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<td class="new_line diff-line-num" data-linenumber="3769" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
3769
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC3769" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @param sets Kmer tables</span></span>
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3562
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<td class="new_line diff-line-num" data-linenumber="3770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
3770
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC3770" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @return Number of bases trimmed</span></span>
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3563
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<td class="new_line diff-line-num" data-linenumber="3771" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
3771
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC3771" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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3564
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<td class="new_line diff-line-num old" data-linenumber="3772" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC3564" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">ktrim</span><span class="o" style="font-weight: 600;">(</span><span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">Read</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">,</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">AbstractKmerTable</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">sets</span><span class="o" style="font-weight: 600;">){</span></span>
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3772
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3772" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">ktrim</span><span class="o" style="font-weight: 600;">(</span><span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">Read</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">,</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">AbstractKmerTable</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">sets</span><span class="o" style="font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">,</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="kd" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">final</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">int</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333;"><span class="idiff addition" style="background-color: #c7f0d2;">start</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">,</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="kd" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">final</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">int</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333;"><span class="idiff right addition" style="background-color: #c7f0d2;">stop</span></span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="old_line diff-line-num" data-linenumber="3565" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
3565
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<td class="new_line diff-line-num" data-linenumber="3773" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
3773
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC3773" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ktrimLeft</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">ktrimRight</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="3566" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
3566
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<td class="new_line diff-line-num" data-linenumber="3774" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
3774
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC3774" 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;">r</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;">r</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="nc" style="color: #458; font-weight: 600;">Tools</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">max</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;">useShortKmers</span> <span class="o" style="font-weight: 600;">?</span> <span class="nc" style="color: #458; font-weight: 600;">Tools</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">min</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">mink</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">storedKmers</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">){</span><span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;}</span></span>
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<td class="old_line diff-line-num" data-linenumber="3567" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
3567
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<td class="new_line diff-line-num" data-linenumber="3775" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
3775
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC3775" 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;">skipR1</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="na" style="color: #008080;">pairnum</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="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">skipR2</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="na" style="color: #008080;">pairnum</span><span class="o" style="font-weight: 600;">()==</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)){</span><span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3577" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -3577,9 +3785,6 @@ public class BBDuk {</td>
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<td class="old_line diff-line-num" data-linenumber="3577" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
3577
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<td class="new_line diff-line-num" data-linenumber="3785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
3785
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC3785" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxLoc</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;">maxLocExclusive</span><span class="o" style="font-weight: 600;">=-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="3578" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
3578
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<td class="new_line diff-line-num" data-linenumber="3786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
3786
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC3786" class="line" lang="java"> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">initialLength</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="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">();</span></span>
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<td class="old_line diff-line-num" data-linenumber="3579" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
3579
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<td class="new_line diff-line-num" data-linenumber="3787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
3787
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC3787" class="line" lang="java"> </span>
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<td class="old_line diff-line-num old" data-linenumber="3580" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
3580
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<td class="new_line diff-line-num old" data-linenumber="3788" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC3580" class="line" lang="java"> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">start</span><span class="o" style="font-weight: 600;">=(</span><span class="n" style="color: #333;">restrictRight</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="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">:</span> <span class="nc" style="color: #458; font-weight: 600;">Tools</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">max</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">bases</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;">restrictRight</span><span class="o" style="font-weight: 600;">));</span></span>
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<td class="old_line diff-line-num old" data-linenumber="3581" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
3581
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<td class="new_line diff-line-num old" data-linenumber="3788" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC3581" class="line" lang="java"> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">stop</span><span class="o" style="font-weight: 600;">=(</span><span class="n" style="color: #333;">restrictLeft</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;">bases</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="nc" style="color: #458; font-weight: 600;">Tools</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">min</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bases</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">restrictLeft</span><span class="o" style="font-weight: 600;">));</span></span>
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<td class="old_line diff-line-num old" data-linenumber="3582" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
3582
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<td class="new_line diff-line-num old" data-linenumber="3788" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC3582" class="line" lang="java"> </span>
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<td class="old_line diff-line-num" data-linenumber="3583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
3583
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<td class="new_line diff-line-num" data-linenumber="3788" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
3788
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC3788" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//Scan for normal kmers</span></span>
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<td class="old_line diff-line-num" data-linenumber="3584" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
3584
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<td class="new_line diff-line-num" data-linenumber="3789" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
3789
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC3789" 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;">start</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;">stop</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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3585
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<td class="new_line diff-line-num" data-linenumber="3790" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
3790
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC3790" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">byte</span> <span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">bases</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</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="4807" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5012" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -4807,9 +5012,9 @@ public class BBDuk {</td>
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<td class="old_line diff-line-num" data-linenumber="4807" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
4807
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<td class="new_line diff-line-num" data-linenumber="5012" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
5012
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC5012" class="line" lang="java"> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">usePairGC</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="4808" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
4808
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<td class="new_line diff-line-num" data-linenumber="5013" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
5013
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC5013" class="line" lang="java"> </span>
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<td class="old_line diff-line-num" data-linenumber="4809" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
4809
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<td class="new_line diff-line-num" data-linenumber="5014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
5014
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC5014" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/** If positive, only look for kmer matches in the leftmost X bases */</span></span>
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<td class="old_line diff-line-num old" data-linenumber="4810" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
4810
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<td class="new_line diff-line-num old" data-linenumber="5015" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC4810" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">restrictLeft</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="4811" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="5015" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
5015
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC5015" class="line" lang="java"> <span class="kd" style="font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">final</span></span><span class="idiff right addition" style="background-color: #c7f0d2;"> </span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">restrictLeft</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="4811" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
4811
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<td class="new_line diff-line-num" data-linenumber="5016" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
5016
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC5016" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/** If positive, only look for kmer matches the rightmost X bases */</span></span>
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<td class="old_line diff-line-num old" data-linenumber="4812" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
4812
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<td class="new_line diff-line-num old" data-linenumber="5017" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC4812" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">restrictRight</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="4813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="5017" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
5017
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC5017" class="line" lang="java"> <span class="kd" style="font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">final</span></span><span class="idiff right addition" style="background-color: #c7f0d2;"> </span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">restrictRight</span><span class="o" style="font-weight: 600;">;</span></span>
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4813
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<td class="new_line diff-line-num" data-linenumber="5018" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
5018
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC5018" class="line" lang="java"> </span>
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<td class="old_line diff-line-num" data-linenumber="4814" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
4814
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<td class="new_line diff-line-num" data-linenumber="5019" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
5019
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC5019" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/** Skip this many initial input reads */</span></span>
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<td class="old_line diff-line-num" data-linenumber="4815" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
4815
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<td class="new_line diff-line-num" data-linenumber="5020" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
5020
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC5020" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">skipreads</span><span class="o" style="font-weight: 600;">;</span></span>
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<a href="https://salsa.debian.org/med-team/bbmap/-/commit/1c662261847da712e5b04b94277f8aa712c37619#635fa9bb7034f5bd7a766f17d0d6cc9b0800f06f" style="color: #1068bf; text-decoration: none;"><strong style="font-weight: bold;">current/jgi/RQCFilter2.java</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="585" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="585" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -585,6 +585,7 @@ public class RQCFilter2 {</td>
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<td class="old_line diff-line-num" data-linenumber="585" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
585
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<td class="new_line diff-line-num" data-linenumber="585" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
585
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC585" class="line" lang="java"> <span class="n" style="color: #333;">microbesUsed</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">appendOutDir</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">microbesUsed</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="586" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
586
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<td class="new_line diff-line-num" data-linenumber="586" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
586
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC586" class="line" lang="java"> <span class="n" style="color: #333;">chloroStatsFile</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">appendOutDir</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">chloroStatsFile</span><span class="o" style="font-weight: 600;">);</span></span>
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587
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<td class="new_line diff-line-num" data-linenumber="587" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
587
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC587" class="line" lang="java"> <span class="n" style="color: #333;">sipStatsFile</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">appendOutDir</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">sipStatsFile</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="588" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="588" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
588
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC588" class="line" lang="java"> <span class="n" style="color: #333;">sipScafStats</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">appendOutDir</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">sipScafStats</span><span class="o" style="font-weight: 600;">);</span></span>
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588
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589
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC589" class="line" lang="java"></span>
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<td class="old_line diff-line-num" data-linenumber="589" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
589
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<td class="new_line diff-line-num" data-linenumber="590" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
590
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC590" class="line" lang="java"> <span class="n" style="color: #333;">cardinalityName</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">appendOutDir</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">cardinalityName</span><span class="o" style="font-weight: 600;">);</span></span>
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590
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591
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC591" class="line" lang="java"> <span class="n" style="color: #333;">adaptersOutFile</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">appendOutDir</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">adaptersOutFile</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="816" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="817" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -816,8 +817,13 @@ public class RQCFilter2 {</td>
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816
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<td class="new_line diff-line-num" data-linenumber="817" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
817
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC817" 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;">"filteredByTile="</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">removeOutDir</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fbtOutFile</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="sc" style="color: #d14;">'\n'</span><span class="o" style="font-weight: 600;">);</span></span>
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817
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<td class="new_line diff-line-num" data-linenumber="818" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
818
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC818" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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818
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<td class="new_line diff-line-num" data-linenumber="819" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
819
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC819" class="line" lang="java"> </span>
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<td class="old_line diff-line-num old" data-linenumber="819" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
819
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<td class="new_line diff-line-num old" data-linenumber="820" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC819" 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;">sipFlag</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">sipStatsFile</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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820
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<td class="new_line diff-line-num old" data-linenumber="820" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC820" 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;">"sipSpikeinStats="</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">removeOutDir</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">sipStatsFile</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="sc" style="color: #d14;">'\n'</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="820" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
820
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC820" 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;">sipFlag</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="821" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
821
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC821" 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;">sipStatsFile</span><span class="o" style="font-weight: 600;">!=</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="822" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
822
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC822" 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;">"sipSpikeinStats="</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">removeOutDir</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">sipStatsFile</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="sc" style="color: #d14;">'\n'</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
823
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC823" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="824" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
824
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC824" 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;">sipScafStats</span><span class="o" style="font-weight: 600;">!=</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="825" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
825
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC825" 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;">"sipScafStats="</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">removeOutDir</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">sipScafStats</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="sc" style="color: #d14;">'\n'</span><span class="o" style="font-weight: 600;">);</span></span>
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826
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC826" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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827
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC827" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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822
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828
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC828" class="line" lang="java"> </span>
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<td class="old_line diff-line-num" data-linenumber="823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
823
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<td class="new_line diff-line-num" data-linenumber="829" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
829
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC829" 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;">chloroMapFlag</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">mitoMapFlag</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">riboMapFlag</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">chloroOutFile</span><span class="o" style="font-weight: 600;">!=</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -1136,15 +1142,15 @@ public class RQCFilter2 {</td>
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<td class="old_line diff-line-num" data-linenumber="1136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1136
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<td class="new_line diff-line-num" data-linenumber="1142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1142
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1142" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="1137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1137
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<td class="new_line diff-line-num" data-linenumber="1143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1143
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1143" class="line" lang="java"> </span>
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<td class="old_line diff-line-num" data-linenumber="1138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1138
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<td class="new_line diff-line-num" data-linenumber="1144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1144
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1144" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//Filter the file to only include specified organisms in the taxlist.</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1139
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<td class="new_line diff-line-num old" data-linenumber="1145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC1139" class="line" lang="java"> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">ref</span><span class="o" style="font-weight: 600;">=</span><span class="nc" style="color: #458; font-weight: 600;">Data</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">findPath</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"?SIP_spikeins.fa.gz"</span><span class="o" style="font-weight: 600;">);</span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right deletion" style="background-color: #fac5cd;">//TODO add to RQCFilterData like others</span></span></span>
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<td class="old_line diff-line-num new" data-linenumber="1140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1145
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1145" class="line" lang="java"> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">ref</span><span class="o" style="font-weight: 600;">=</span><span class="nc" style="color: #458; font-weight: 600;">Data</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">findPath</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"?SIP_spikeins.fa.gz"</span><span class="o" style="font-weight: 600;">);</span></span>
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1140
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<td class="new_line diff-line-num" data-linenumber="1146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1146
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1146" class="line" lang="java"> </span>
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<td class="old_line diff-line-num" data-linenumber="1141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1141
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<td class="new_line diff-line-num" data-linenumber="1147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1147
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1147" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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1142
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<td class="new_line diff-line-num" data-linenumber="1148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1148
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1148" class="line" lang="java"> <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 class="n" style="color: #333;">args</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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<td class="old_line diff-line-num" data-linenumber="1143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1143
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<td class="new_line diff-line-num" data-linenumber="1149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1149
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1149" class="line" lang="java"> <span class="n" style="color: #333;">args</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="s" style="color: #d14;">"covstats="</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">sipStatsFile</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="1144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1144
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<td class="new_line diff-line-num" data-linenumber="1150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1150
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1150" class="line" lang="java"> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">addToOtherStats</span><span class="o" style="font-weight: 600;">=(</span><span class="n" style="color: #333;">sipStatsFile</span><span class="o" style="font-weight: 600;">==</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1145
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<td class="new_line diff-line-num old" data-linenumber="1151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC1145" class="line" lang="java"> <span class="n" style="color: #333;">decontamByMapping</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">in1z</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">in2z</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">out1z</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">out2z</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="s" style="color: #d14;"><span class="idiff left deletion" style="background-color: #fac5cd;">"</span>sipScafStats<span class="idiff right deletion" style="background-color: #fac5cd;">.txt"</span></span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">inPrefix</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">outPrefix</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">ref</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">step</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">addToOtherStats</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1151
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1151" class="line" lang="java"> <span class="n" style="color: #333;">decontamByMapping</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">in1z</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">in2z</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">out1z</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">out2z</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;">sipScafStats</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">inPrefix</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">outPrefix</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">ref</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">step</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">addToOtherStats</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="1146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1146
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<td class="new_line diff-line-num" data-linenumber="1152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1152
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1152" 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;">addToOtherStats</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1147
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<td class="new_line diff-line-num old" data-linenumber="1153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC1147" class="line" lang="java"> <span class="n" style="color: #333;">filterstats</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseSip</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;"><span class="idiff left deletion" style="background-color: #fac5cd;">"</span>sipScafStats<span class="idiff right deletion" style="background-color: #fac5cd;">.txt"</span></span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1153
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1153" class="line" lang="java"> <span class="n" style="color: #333;">filterstats</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseSip</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">sipScafStats</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="1148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1148
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<td class="new_line diff-line-num" data-linenumber="1154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1154
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1154" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">filterstats</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 class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="1149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1149
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<td class="new_line diff-line-num" data-linenumber="1155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1155
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1155" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="1150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1150
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<td class="new_line diff-line-num" data-linenumber="1156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1156
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1156" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3982" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3988" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -3982,6 +3988,7 @@ public class RQCFilter2 {</td>
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<td class="old_line diff-line-num" data-linenumber="3982" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
3982
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<td class="new_line diff-line-num" data-linenumber="3988" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
3988
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC3988" 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;">microbesUsed</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"microbesUsed.txt"</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="3983" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
3983
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<td class="new_line diff-line-num" data-linenumber="3989" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
3989
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC3989" 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;">chloroStatsFile</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"chloroStats.txt"</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="3984" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
3984
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<td class="new_line diff-line-num" data-linenumber="3990" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
3990
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC3990" 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;">sipStatsFile</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"sipSpikeinStats.txt"</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="3985" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="3991" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3991
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3991" 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;">sipScafStats</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"sipScafStats.txt"</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="3985" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
3985
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<td class="new_line diff-line-num" data-linenumber="3992" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
3992
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC3992" 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;">nexteraStats</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"nexteraStats.txt"</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="3986" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
3986
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<td class="new_line diff-line-num" data-linenumber="3993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
3993
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC3993" 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;">ihistName</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"ihist_merge.txt"</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="3987" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
3987
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<td class="new_line diff-line-num" data-linenumber="3994" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
3994
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC3994" 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;">khistName</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"khist.txt"</span><span class="o" style="font-weight: 600;">;</span></span>
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<li id="c1eb3ba3e50eb26c73088b4da40ccd2361d064a3">
<a href="https://salsa.debian.org/med-team/bbmap/-/commit/1c662261847da712e5b04b94277f8aa712c37619#c1eb3ba3e50eb26c73088b4da40ccd2361d064a3" style="color: #1068bf; text-decoration: none;"><strong style="font-weight: bold;">current/jgi/RQCFilterStats.java</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -93,10 +93,6 @@ public class RQCFilterStats {</td>
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<td class="old_line diff-line-num" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
93
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<td class="new_line diff-line-num" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
93
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC93" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
94
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<td class="new_line diff-line-num" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
94
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC94" class="line" lang="java"> </span>
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<td class="old_line diff-line-num" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
95
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95
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC95" 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;">toString</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">skipAssertion</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="old_line diff-line-num old" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
96
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<td class="new_line diff-line-num old" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC96" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">skipAssertion</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">readsIn</span><span class="o" style="font-weight: 600;">>=</span><span class="n" style="color: #333;">readsOut</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">toString</span><span class="o" style="font-weight: 600;">(</span><span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
97
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<td class="new_line diff-line-num old" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC97" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">skipAssertion</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">basesIn</span><span class="o" style="font-weight: 600;">>=</span><span class="n" style="color: #333;">basesOut</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">toString</span><span class="o" style="font-weight: 600;">(</span><span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num old" 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: inherit;" align="right" bgcolor="#f9d7dc">
98
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<td class="new_line diff-line-num old" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC98" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">skipAssertion</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">readsIn</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">totalReadsRemoved</span><span class="o" style="font-weight: 600;">()==</span><span class="n" style="color: #333;">readsOut</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">toString</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 class="s" style="color: #d14;">"\n\ntrr="</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">totalReadsRemoved</span><span class="o" style="font-weight: 600;">()+</span><span class="s" style="color: #d14;">"\nri="</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">readsIn</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"\nro="</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">readsOut</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
99
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<td class="new_line diff-line-num old" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC99" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">skipAssertion</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">basesIn</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">totalBasesRemoved</span><span class="o" style="font-weight: 600;">()==</span><span class="n" style="color: #333;">basesOut</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">toString</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 class="s" style="color: #d14;">"\n"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">basesIn</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;">totalBasesRemoved</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;">basesOut</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
100
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<td class="new_line diff-line-num" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
96
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC96" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">StringBuilder</span> <span class="n" style="color: #333;">sb</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;">StringBuilder</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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<td class="old_line diff-line-num" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
101
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<td class="new_line diff-line-num" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
97
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC97" 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;">"#Class\tReads\tBases\tReadPct\tBasePct\tNotes\n"</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num" 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: inherit;" align="right" bgcolor="#fafafa">
102
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<td class="new_line diff-line-num" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
98
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC98" 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;">format</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Input"</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">readsIn</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">basesIn</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">readsIn</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">basesIn</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="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -120,6 +116,12 @@ public class RQCFilterStats {</td>
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<td class="old_line diff-line-num" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
120
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<td class="new_line diff-line-num" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
116
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC116" 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;">format</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Dog"</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">readsDog</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">basesDog</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">readsIn</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">basesIn</span><span class="o" style="font-weight: 600;">));</span></span>
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<td class="old_line diff-line-num" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
121
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<td class="new_line diff-line-num" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
117
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC117" 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;">format</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Microbe"</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">readsMicrobe</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">basesMicrobe</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">readsIn</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">basesIn</span><span class="o" style="font-weight: 600;">));</span></span>
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<td class="old_line diff-line-num" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
122
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<td class="new_line diff-line-num" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
118
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC118" 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;">format</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Other"</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">readsOther</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">basesOther</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">readsIn</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">basesIn</span><span class="o" style="font-weight: 600;">));</span></span>
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<td class="old_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
119
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC119" class="line" lang="java"> </span>
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<td class="old_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
120
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC120" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">skipAssertion</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">readsIn</span><span class="o" style="font-weight: 600;">>=</span><span class="n" style="color: #333;">readsOut</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">toString</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 class="s" style="color: #d14;">"\n\nsb:\n"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">sb</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="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
121
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC121" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">skipAssertion</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">basesIn</span><span class="o" style="font-weight: 600;">>=</span><span class="n" style="color: #333;">basesOut</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">toString</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 class="s" style="color: #d14;">"\n\n"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">sb</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="old_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
122
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC122" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">skipAssertion</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">readsIn</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">totalReadsRemoved</span><span class="o" style="font-weight: 600;">()==</span><span class="n" style="color: #333;">readsOut</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">toString</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 class="s" style="color: #d14;">"\n\ntrr="</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">totalReadsRemoved</span><span class="o" style="font-weight: 600;">()+</span><span class="s" style="color: #d14;">"\nri="</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">readsIn</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"\nro="</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">readsOut</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"\n\nsb:\n"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">sb</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="old_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
123
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC123" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">skipAssertion</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">basesIn</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">totalBasesRemoved</span><span class="o" style="font-weight: 600;">()==</span><span class="n" style="color: #333;">basesOut</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">toString</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 class="s" style="color: #d14;">"\n"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">basesIn</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;">totalBasesRemoved</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;">basesOut</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"\n\nsb:\n"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">sb</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="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
124
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC124" class="line" lang="java"> </span>
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123
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<td class="new_line diff-line-num" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
125
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC125" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">sb</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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124
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126
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC126" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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125
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127
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC127" class="line" lang="java"> </span>
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<a href="https://salsa.debian.org/med-team/bbmap/-/commit/1c662261847da712e5b04b94277f8aa712c37619#187cd9d49b7c25c10731650b44504aafb9eb2fa1" style="color: #1068bf; text-decoration: none;"><strong style="font-weight: bold;">current/shared/Parser.java</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1418" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1418" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -1418,6 +1418,10 @@ public class Parser {</td>
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<td class="old_line diff-line-num" data-linenumber="1418" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1418
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<td class="new_line diff-line-num" data-linenumber="1418" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1418
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1418" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">byte</span> <span class="n" style="color: #333;">qout</span><span class="o" style="font-weight: 600;">=-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="1419" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1419
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<td class="new_line diff-line-num" data-linenumber="1419" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1419
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1419" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">parsedQuality</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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1420
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<td class="new_line diff-line-num" data-linenumber="1420" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1420
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1420" class="line" lang="java"> </span>
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<td class="old_line diff-line-num new" data-linenumber="1421" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1421" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1421
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1421" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">setQuality</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;">x</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1422" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1422
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1422" class="line" lang="java"> <span class="n" style="color: #333;">qin</span><span class="o" style="font-weight: 600;">=(</span><span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="o" style="font-weight: 600;">)</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">;</span></span>
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1423
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1423" class="line" lang="java"> <span class="n" style="color: #333;">parsedQuality</span><span class="o" style="font-weight: 600;">=(</span><span class="n" style="color: #333;">x</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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1424
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1424" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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1421
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<td class="new_line diff-line-num" data-linenumber="1425" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1425
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1425" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">processQuality</span><span class="o" style="font-weight: 600;">(){</span></span>
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<td class="old_line diff-line-num" data-linenumber="1422" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1422
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<td class="new_line diff-line-num" data-linenumber="1426" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1426
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1426" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// assert(parsedQuality);</span></span>
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<td class="old_line diff-line-num" data-linenumber="1423" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1423
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<td class="new_line diff-line-num" data-linenumber="1427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1427
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1427" 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;">parsedQuality</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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<a href="https://salsa.debian.org/med-team/bbmap/-/commit/1c662261847da712e5b04b94277f8aa712c37619#ef3b3e694c0bbaa70bf4c35a23c328ce44020fb6" style="color: #1068bf; text-decoration: none;"><strong style="font-weight: bold;">current/shared/Shared.java</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -125,8 +125,8 @@ public class Shared {</td>
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<td class="old_line diff-line-num" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
125
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<td class="new_line diff-line-num" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
125
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC125" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="no" style="color: #008080;">GAPCOST</span><span class="o" style="font-weight: 600;">=</span><span class="nc" style="color: #458; font-weight: 600;">Tools</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">max</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="no" style="color: #008080;">GAPLEN</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">64</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
126
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<td class="new_line diff-line-num" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
126
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC126" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">byte</span> <span class="no" style="color: #008080;">GAPC</span><span class="o" style="font-weight: 600;">=</span><span class="sc" style="color: #d14;">'-'</span><span class="o" style="font-weight: 600;">;</span></span>
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127
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<td class="new_line diff-line-num" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
127
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC127" class="line" lang="java"> </span>
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<td class="old_line diff-line-num old" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
128
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<td class="new_line diff-line-num old" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC128" 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="no" style="color: #008080;">BBMAP_VERSION_STRING</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"38.9<span class="idiff left right deletion" style="background-color: #fac5cd;">6</span>"</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
129
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<td class="new_line diff-line-num old" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC129" 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="no" style="color: #008080;">BBMAP_VERSION_NAME</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"<span class="idiff left right deletion" style="background-color: #fac5cd;">Return Tru</span>e"</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
128
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC128" 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="no" style="color: #008080;">BBMAP_VERSION_STRING</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"38.9<span class="idiff left right addition" style="background-color: #c7f0d2;">7</span>"</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
129
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC129" 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="no" style="color: #008080;">BBMAP_VERSION_NAME</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"<span class="idiff left right addition" style="background-color: #c7f0d2;">Honeybe</span>e"</span><span class="o" style="font-weight: 600;">;</span></span>
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130
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<td class="new_line diff-line-num" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
130
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC130" class="line" lang="java"> </span>
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<td class="old_line diff-line-num" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
131
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<td class="new_line diff-line-num" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
131
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC131" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="no" style="color: #008080;">TRIM_READ_COMMENTS</span><span class="o" style="font-weight: 600;">=</span><span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
132
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<td class="new_line diff-line-num" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
132
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC132" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="no" style="color: #008080;">TRIM_RNAME</span><span class="o" style="font-weight: 600;">=</span><span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span> <span class="c1" style="color: #998; font-style: italic;">//For mapped sam reads</span></span>
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<a href="https://salsa.debian.org/med-team/bbmap/-/commit/1c662261847da712e5b04b94277f8aa712c37619#14fe639b07fd847461a2af0e6f8941d849848429" style="color: #1068bf; text-decoration: none;"><strong style="font-weight: bold;">current/stream/FASTQ.java</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -178,6 +178,7 @@ public class FASTQ {</td>
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<td class="old_line diff-line-num" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
178
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<td class="new_line diff-line-num" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
178
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC178" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span><span class="k" style="font-weight: 600;">else</span><span class="o" style="font-weight: 600;">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
179
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<td class="new_line diff-line-num" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
179
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC179" 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;">warnQualityChange</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;">"Changed from ASCII-64 to ASCII-33 due to read of length "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">bases</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" while prescanning."</span><span class="o" style="font-weight: 600;">);}</span></span>
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<td class="old_line diff-line-num" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
180
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<td class="new_line diff-line-num" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
180
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC180" class="line" lang="java"> <span class="no" style="color: #008080;">ASCII_OFFSET</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">33</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
181
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC181" class="line" lang="java"> <span class="no" style="color: #008080;">SET_QIN</span><span class="o" style="font-weight: 600;">=</span><span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
181
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<td class="new_line diff-line-num" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
182
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC182" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
182
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<td class="new_line diff-line-num" 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: inherit;" align="right" bgcolor="#fafafa">
183
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC183" class="line" lang="java"> <span class="no" style="color: #008080;">DETECT_QUALITY</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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183
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184
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC184" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="549" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="550" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -549,12 +550,15 @@ public class FASTQ {</td>
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<td class="old_line diff-line-num" data-linenumber="549" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
549
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<td class="new_line diff-line-num" data-linenumber="550" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
550
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC550" class="line" lang="java"> <span class="no" style="color: #008080;">ASCII_OFFSET</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">33</span><span class="o" style="font-weight: 600;">;</span></span>
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550
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<td class="new_line diff-line-num" data-linenumber="551" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
551
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC551" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="551" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
551
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<td class="new_line diff-line-num" data-linenumber="552" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
552
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC552" class="line" lang="java"> <span class="no" style="color: #008080;">DETECT_QUALITY</span><span class="o" style="font-weight: 600;">=</span><span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="552" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="553" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
553
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC553" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// System.err.println("A: "+numericID+": "+bases.length);</span></span>
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552
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<td class="new_line diff-line-num" data-linenumber="554" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
554
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC554" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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553
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<td class="new_line diff-line-num" data-linenumber="555" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
555
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC555" class="line" lang="java"> </span>
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554
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<td class="new_line diff-line-num" data-linenumber="556" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
556
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC556" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// assert(false) : Arrays.toString(quals);</span></span>
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555
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<td class="new_line diff-line-num" data-linenumber="557" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
557
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC557" 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;">quals</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>
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556
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<td class="new_line diff-line-num" data-linenumber="558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
558
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC558" class="line" lang="java"> <span class="n" style="color: #333;">quals</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="no" style="color: #008080;">ASCII_OFFSET</span><span class="o" style="font-weight: 600;">;</span> <span class="c1" style="color: #998; font-style: italic;">//Convert from ASCII33 to native.</span></span>
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557
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<td class="new_line diff-line-num" data-linenumber="559" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
559
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC559" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="no" style="color: #008080;">DETECT_QUALITY</span> <span class="o" style="font-weight: 600;">&&</span> <span class="no" style="color: #008080;">ASCII_OFFSET</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">33</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">quals</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="no" style="color: #008080;">QUAL_THRESH</span> <span class="cm" style="color: #998; font-style: italic;">/*|| (bases[i]=='N' && quals[i]>20)*/</span><span class="o" style="font-weight: 600;">)){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
560
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC560" class="line" lang="java"></span>
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<td class="old_line diff-line-num new" data-linenumber="558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="561" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
561
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC561" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// System.err.println("B: "+numericID+": "+bases.length);</span></span>
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558
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<td class="new_line diff-line-num" data-linenumber="562" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
562
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC562" 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;">warnQualityChange</span><span class="o" style="font-weight: 600;">){</span></span>
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559
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<td class="new_line diff-line-num" data-linenumber="563" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
563
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC563" 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;">numericID</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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560
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<td class="new_line diff-line-num" data-linenumber="564" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
564
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC564" 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;">"Changed from ASCII-33 to ASCII-64 on input "</span><span class="o" style="font-weight: 600;">+((</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">)</span><span class="n" style="color: #333;">quals</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">])+</span><span class="s" style="color: #d14;">": "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">quals</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]+</span><span class="s" style="color: #d14;">" -> "</span><span class="o" style="font-weight: 600;">+(</span><span class="n" style="color: #333;">quals</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;">31</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="651" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="655" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -651,6 +655,29 @@ public class FASTQ {</td>
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651
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655
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC655" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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652
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656
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC656" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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653
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<td class="new_line diff-line-num" data-linenumber="657" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
657
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC657" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span><span class="k" style="font-weight: 600;">else</span><span class="o" style="font-weight: 600;">{</span></span>
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658
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC658" class="line" lang="java"> </span>
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<td class="old_line diff-line-num new" data-linenumber="654" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="659" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
659
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC659" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//Prevents problems with PacBio's weird quality numbers. Usually.</span></span>
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<td class="old_line diff-line-num new" data-linenumber="654" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="660" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
660
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC660" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="no" style="color: #008080;">DETECT_QUALITY</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">numericID</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="c1" style="color: #998; font-style: italic;">//first read</span></span>
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<td class="new_line diff-line-num new" data-linenumber="661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
661
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC661" 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;">byte</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">bf</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextLine</span><span class="o" style="font-weight: 600;">();</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">!=</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">bf</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextLine</span><span class="o" style="font-weight: 600;">()){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
662
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC662" 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;">cntr</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;">s</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="no" style="color: #008080;">MIN_LENGTH_TO_FORCE_ASCII_33</span><span class="o" style="font-weight: 600;">){</span><span class="c1" style="color: #998; font-style: italic;">//Chances of ASCII-64 are vanishingly small</span></span>
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<td class="new_line diff-line-num new" data-linenumber="663" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
663
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC663" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// SET_QIN=true;</span></span>
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664
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC664" class="line" lang="java"> <span class="no" style="color: #008080;">DETECT_QUALITY</span><span class="o" style="font-weight: 600;">=</span><span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="665" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
665
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC665" class="line" lang="java"> <span class="no" style="color: #008080;">ASCII_OFFSET</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">33</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="666" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
666
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC666" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="667" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
667
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC667" class="line" lang="java"> <span class="n" style="color: #333;">quad</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">cntr</span><span class="o" style="font-weight: 600;">]=</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="668" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
668
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC668" class="line" lang="java"> <span class="n" style="color: #333;">cntr</span><span class="o" style="font-weight: 600;">++;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="669" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
669
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC669" 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;">cntr</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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<td class="new_line diff-line-num new" data-linenumber="670" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
670
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC670" class="line" lang="java"> <span class="n" style="color: #333;">cntr</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="new_line diff-line-num new" data-linenumber="671" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
671
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC671" class="line" lang="java"> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">Read</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">quadToRead_slow</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">quad</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">bf</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">numericID</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">flag</span><span class="o" style="font-weight: 600;">);</span></span>
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672
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC672" class="line" lang="java"> </span>
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<td class="new_line diff-line-num new" data-linenumber="673" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
673
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC673" class="line" lang="java"> <span class="n" style="color: #333;">list</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;">r</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="674" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
674
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC674" class="line" lang="java"> <span class="n" style="color: #333;">added</span><span class="o" style="font-weight: 600;">++;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="675" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
675
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC675" class="line" lang="java"> <span class="n" style="color: #333;">numericID</span><span class="o" style="font-weight: 600;">++;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="676" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
676
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC676" 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;">added</span><span class="o" style="font-weight: 600;">>=</span><span class="n" style="color: #333;">maxReadsToReturn</span><span class="o" style="font-weight: 600;">){</span><span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">list</span><span class="o" style="font-weight: 600;">;}</span></span>
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677
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC677" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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678
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC678" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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679
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC679" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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680
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC680" class="line" lang="java"> </span>
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681
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC681" 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;">byte</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">bf</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextLine</span><span class="o" style="font-weight: 600;">();</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">!=</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">bf</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextLine</span><span class="o" style="font-weight: 600;">()){</span></span>
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655
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<td class="new_line diff-line-num" data-linenumber="682" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
682
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC682" class="line" lang="java"> <span class="n" style="color: #333;">quad</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">cntr</span><span class="o" style="font-weight: 600;">]=</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">;</span></span>
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656
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683
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC683" class="line" lang="java"> <span class="n" style="color: #333;">cntr</span><span class="o" style="font-weight: 600;">++;</span></span>
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<a href="https://salsa.debian.org/med-team/bbmap/-/commit/1c662261847da712e5b04b94277f8aa712c37619#a7cccac0c9e3ce8fcea270125d8329c409c781d1" style="color: #1068bf; text-decoration: none;"><strong style="font-weight: bold;">current/tax/GiToTaxid.java</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -88,36 +88,24 @@ public class GiToTaxid {</td>
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88
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<td class="new_line diff-line-num" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
88
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC88" class="line" lang="java"> </span>
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<td class="old_line diff-line-num" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
89
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<td class="new_line diff-line-num" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
89
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC89" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">parseGiToTaxid</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;">s</span><span class="o" style="font-weight: 600;">){</span><span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">parseGiToTaxid</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">,</span> <span class="sc" style="color: #d14;">'|'</span><span class="o" style="font-weight: 600;">);}</span></span>
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<td class="old_line diff-line-num" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
90
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<td class="new_line diff-line-num" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
90
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC90" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">parseGiToTaxid</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;">s</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">delimiter</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="old_line diff-line-num old" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
91
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<td class="new_line diff-line-num old" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC91" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">parseGiNumber</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">delimiter</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
92
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<td class="new_line diff-line-num old" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC92" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">x</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;">s</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
93
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<td class="new_line diff-line-num old" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC93" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">array</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="s" style="color: #d14;">"To use gi numbers, you must load a gi table."</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
94
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<td class="new_line diff-line-num old" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC94" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// if(x>=array.length || array[x]<0){x=(int)(Math.random()*array.length);} //Test to make sure array is nonempty.</span></span>
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<td class="old_line diff-line-num old" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
95
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<td class="new_line diff-line-num old" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<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;">x</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;">x</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">array</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="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">array</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">];}</span></span>
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<td class="old_line diff-line-num old" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
96
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<td class="new_line diff-line-num old" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC96" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">array</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="s" style="color: #d14;">"The GI number "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" is too big.\n"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
97
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<td class="new_line diff-line-num old" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC97" class="line" lang="java"> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"Please update the gi table with the latest version from NCBI as per the instructions in gitable.sh.\n"</span></span>
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<td class="old_line diff-line-num old" 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: inherit;" align="right" bgcolor="#f9d7dc">
98
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<td class="new_line diff-line-num old" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC98" class="line" lang="java"> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"To ignore this problem, please run with the -da flag.\n"</span><span class="o" style="font-weight: 600;">;</span></span>
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99
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<td class="new_line diff-line-num old" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC99" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
91
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC91" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">parseGiNumber</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">delimiter</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
92
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC92" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">x</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;">x</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;">s</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
93
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC93" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="nf" style="color: #900; font-weight: 600;">getID</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
100
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<td class="new_line diff-line-num" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
94
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC94" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
101
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<td class="new_line diff-line-num" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
95
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC95" class="line" lang="java"> </span>
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<td class="old_line diff-line-num" 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: inherit;" align="right" bgcolor="#fafafa">
102
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<td class="new_line diff-line-num" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
96
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC96" class="line" lang="java"></span>
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<td class="old_line diff-line-num" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
103
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<td class="new_line diff-line-num" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
97
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC97" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">parseGiToTaxid</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">){</span><span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">parseGiToTaxid</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">,</span> <span class="sc" style="color: #d14;">'|'</span><span class="o" style="font-weight: 600;">);}</span></span>
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<td class="old_line diff-line-num" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
104
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<td class="new_line diff-line-num" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
98
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC98" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">parseGiToTaxid</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">delimiter</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="old_line diff-line-num old" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
105
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<td class="new_line diff-line-num old" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC105" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">parseGiNumber</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">delimiter</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
106
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<td class="new_line diff-line-num old" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC106" 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;">x</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="n" style="color: #333;">array</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">];}</span></span>
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<td class="old_line diff-line-num old" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
107
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<td class="new_line diff-line-num old" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC107" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
99
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC99" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">parseGiNumber</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">delimiter</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
100
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC100" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">x</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;">1</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">getID</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
108
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<td class="new_line diff-line-num" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
101
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC101" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
109
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<td class="new_line diff-line-num" 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: inherit;" align="right" bgcolor="#fafafa">
102
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC102" class="line" lang="java"> </span>
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<td class="old_line diff-line-num" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
110
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<td class="new_line diff-line-num" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
103
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC103" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/** Parse a gi number, or return -1 if formatted incorrectly. */</span></span>
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<td class="old_line diff-line-num old" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
111
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<td class="new_line diff-line-num old" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC111" class="line" lang="java"> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right deletion" style="background-color: #fac5cd;">int</span></span> <span class="nf" style="color: #900; font-weight: 600;">parseGiNumber</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;">s</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">delimiter</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="old_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
104
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC104" class="line" lang="java"> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right addition" style="background-color: #c7f0d2;">long</span></span> <span class="nf" style="color: #900; font-weight: 600;">parseGiNumber</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;">s</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">delimiter</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="old_line diff-line-num" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
112
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<td class="new_line diff-line-num" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
105
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC105" 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;">s</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;">s</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="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;}</span></span>
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<td class="old_line diff-line-num old" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
113
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<td class="new_line diff-line-num old" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC113" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// System.err.println("a");</span></span>
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<td class="old_line diff-line-num" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
114
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<td class="new_line diff-line-num" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
106
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC106" 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;">s</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">charAt</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="sc" style="color: #d14;">'>'</span><span class="o" style="font-weight: 600;">){</span><span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">getID</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">substring</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;">delimiter</span><span class="o" style="font-weight: 600;">);}</span></span>
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<td class="old_line diff-line-num old" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
115
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<td class="new_line diff-line-num old" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC115" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// System.err.println("b");</span></span>
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<td class="old_line diff-line-num" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
116
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<td class="new_line diff-line-num" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
107
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC107" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">s</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;">"gi"</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 class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;}</span></span>
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<td class="old_line diff-line-num old" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
117
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<td class="new_line diff-line-num old" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC117" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// System.err.println("c");</span></span>
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<td class="old_line diff-line-num old" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
118
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<td class="new_line diff-line-num old" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC118" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// System.err.println("d");</span></span>
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<td class="old_line diff-line-num" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
119
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<td class="new_line diff-line-num" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
108
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC108" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">initial</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">indexOf</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">delimiter</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
120
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<td class="new_line diff-line-num old" 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: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC120" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// System.err.println("e");</span></span>
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<td class="old_line diff-line-num" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
121
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<td class="new_line diff-line-num" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
109
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC109" 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;">initial</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="old_line diff-line-num" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
122
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<td class="new_line diff-line-num" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
110
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <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;">delimiter</span><span class="o" style="font-weight: 600;">!=</span><span class="sc" style="color: #d14;">'~'</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="old_line diff-line-num" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
123
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<td class="new_line diff-line-num" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
111
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC111" class="line" lang="java"> <span class="n" style="color: #333;">delimiter</span><span class="o" style="font-weight: 600;">=</span><span class="sc" style="color: #d14;">'~'</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -128,21 +116,16 @@ public class GiToTaxid {</td>
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128
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<td class="new_line diff-line-num" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
116
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC116" class="line" lang="java"> <span class="n" style="color: #333;">initial</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">indexOf</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">delimiter</span><span class="o" style="font-weight: 600;">);</span></span>
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129
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<td class="new_line diff-line-num" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
117
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC117" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
130
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<td class="new_line diff-line-num" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
118
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC118" 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;">initial</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 class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;}</span></span>
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<td class="old_line diff-line-num old" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
131
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<td class="new_line diff-line-num old" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC131" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// System.err.println("f");</span></span>
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<td class="old_line diff-line-num old" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
132
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<td class="new_line diff-line-num old" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC132" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// System.err.println("g");</span></span>
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<td class="old_line diff-line-num" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
133
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<td class="new_line diff-line-num" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
119
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC119" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="old_line diff-line-num old" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
134
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<td class="new_line diff-line-num old" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC134" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// System.err.println("h");</span></span>
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<td class="old_line diff-line-num" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
135
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<td class="new_line diff-line-num" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
120
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC120" 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;">Tools</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isDigit</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">charAt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">initial</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">))){</span><span class="k" style="font-weight: 600;">return</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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136
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<td class="new_line diff-line-num old" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC136" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// System.err.println("i");</span></span>
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<td class="old_line diff-line-num" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
137
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<td class="new_line diff-line-num" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
121
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC121" class="line" lang="java"> </span>
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<td class="old_line diff-line-num old" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
138
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<td class="new_line diff-line-num old" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC138" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right deletion" style="background-color: #fac5cd;">int</span></span> <span class="n" style="color: #333;">number</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="old_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
122
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC122" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right addition" style="background-color: #c7f0d2;">long</span></span> <span class="n" style="color: #333;">number</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="old_line diff-line-num" 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: inherit;" align="right" bgcolor="#fafafa">
139
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<td class="new_line diff-line-num" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
123
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <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="n" style="color: #333;">initial</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;">s</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>
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<td class="old_line diff-line-num" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
140
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<td class="new_line diff-line-num" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
124
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC124" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">charAt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
141
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<td class="new_line diff-line-num" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
125
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC125" 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;">c</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">delimiter</span><span class="o" style="font-weight: 600;">){</span><span class="k" style="font-weight: 600;">break</span><span class="o" style="font-weight: 600;">;}</span></span>
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<td class="old_line diff-line-num" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
142
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<td class="new_line diff-line-num" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
126
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC126" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Tools</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isDigit</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">));</span></span>
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<td class="old_line diff-line-num" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
143
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<td class="new_line diff-line-num" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
127
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC127" class="line" lang="java"> <span class="n" style="color: #333;">number</span><span class="o" style="font-weight: 600;">=(</span><span class="n" style="color: #333;">number</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;">c</span><span class="o" style="font-weight: 600;">-</span><span class="sc" style="color: #d14;">'0'</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
144
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<td class="new_line diff-line-num" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
128
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC128" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="old_line diff-line-num old" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
145
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<td class="new_line diff-line-num old" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC145" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// System.err.println("j: "+number);</span></span>
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<td class="old_line diff-line-num" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
146
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<td class="new_line diff-line-num" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
129
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC129" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">number</span><span class="o" style="font-weight: 600;">;</span></span>
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147
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130
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC130" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
148
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131
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC131" class="line" lang="java"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -173,15 +156,14 @@ public class GiToTaxid {</td>
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<td class="old_line diff-line-num" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
173
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<td class="new_line diff-line-num" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
156
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC156" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">getID</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;">s</span><span class="o" style="font-weight: 600;">){</span><span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">getID</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">,</span> <span class="sc" style="color: #d14;">'|'</span><span class="o" style="font-weight: 600;">);}</span></span>
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<td class="old_line diff-line-num" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
174
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<td class="new_line diff-line-num" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
157
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC157" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/** Get the taxID from a header starting with a taxID or gi number */</span></span>
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<td class="old_line diff-line-num" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
175
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<td class="new_line diff-line-num" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
158
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC158" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">getID</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;">s</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">delimiter</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="old_line diff-line-num old" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
176
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<td class="new_line diff-line-num old" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC176" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right deletion" style="background-color: #fac5cd;">int</span></span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">parseTaxidNumber</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">delimiter</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num old" 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: inherit;" align="right" bgcolor="#f9d7dc">
177
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<td class="new_line diff-line-num old" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC177" 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;">x</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="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">;}</span></span>
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<td class="old_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
159
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC159" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right addition" style="background-color: #c7f0d2;">long</span></span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">parseTaxidNumber</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">delimiter</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
160
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC160" 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;">x</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 class="idiff left addition" style="background-color: #c7f0d2;">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">int</span></span><span class="o" style="font-weight: 600;"><span class="idiff right addition" style="background-color: #c7f0d2;">)</span></span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">;}</span></span>
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<td class="old_line diff-line-num" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
178
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<td class="new_line diff-line-num" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
161
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC161" class="line" lang="java"> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">parseGiNumber</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">delimiter</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num old" 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: inherit;" align="right" bgcolor="#f9d7dc">
179
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<td class="new_line diff-line-num old" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC179" 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;">x</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="n" style="color: #333;">array</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">];}</span></span>
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180
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<td class="new_line diff-line-num old" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC180" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
162
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC162" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">x</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;">1</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">getID</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
181
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<td class="new_line diff-line-num" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
163
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC163" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
182
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<td class="new_line diff-line-num" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
164
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC164" class="line" lang="java"> </span>
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<td class="old_line diff-line-num" 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: inherit;" align="right" bgcolor="#fafafa">
183
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<td class="new_line diff-line-num" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
165
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC165" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/** Parse a gi number, or return -1 if formatted incorrectly. */</span></span>
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<td class="old_line diff-line-num old" 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: inherit;" align="right" bgcolor="#f9d7dc">
184
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<td class="new_line diff-line-num old" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC184" class="line" lang="java"> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right deletion" style="background-color: #fac5cd;">int</span></span> <span class="nf" style="color: #900; font-weight: 600;">parseGiNumber</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">delimiter</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="old_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
166
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC166" class="line" lang="java"> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right addition" style="background-color: #c7f0d2;">long</span></span> <span class="nf" style="color: #900; font-weight: 600;">parseGiNumber</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">delimiter</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="old_line diff-line-num" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
185
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<td class="new_line diff-line-num" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
167
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC167" 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;">s</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;">s</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="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;}</span></span>
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<td class="old_line diff-line-num" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
186
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<td class="new_line diff-line-num" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
168
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC168" 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;">Tools</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="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"gi"</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="nc" style="color: #458; font-weight: 600;">Tools</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="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">">gi"</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 class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;}</span></span>
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<td class="old_line diff-line-num" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
187
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<td class="new_line diff-line-num" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
169
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC169" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">initial</span><span class="o" style="font-weight: 600;">=</span><span class="nc" style="color: #458; font-weight: 600;">Tools</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">indexOf</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">,</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="o" style="font-weight: 600;">)</span><span class="n" style="color: #333;">delimiter</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="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -192,7 +174,7 @@ public class GiToTaxid {</td>
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<td class="old_line diff-line-num" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
192
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<td class="new_line diff-line-num" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
174
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC174" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
193
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<td class="new_line diff-line-num" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
175
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC175" 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;">Tools</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isDigit</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">initial</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">])){</span><span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;}</span></span>
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<td class="old_line diff-line-num" 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: inherit;" align="right" bgcolor="#fafafa">
194
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<td class="new_line diff-line-num" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
176
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC176" class="line" lang="java"> </span>
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<td class="old_line diff-line-num old" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
195
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<td class="new_line diff-line-num old" 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: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC195" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right deletion" style="background-color: #fac5cd;">int</span></span> <span class="n" style="color: #333;">number</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="old_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
177
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC177" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right addition" style="background-color: #c7f0d2;">long</span></span> <span class="n" style="color: #333;">number</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="old_line diff-line-num" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
196
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<td class="new_line diff-line-num" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
178
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC178" 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;">initial</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;">s</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>
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<td class="old_line diff-line-num" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
197
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<td class="new_line diff-line-num" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
179
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC179" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">byte</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">];</span></span>
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<td class="old_line diff-line-num" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
198
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<td class="new_line diff-line-num" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
180
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC180" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">delimiter</span><span class="o" style="font-weight: 600;">){</span><span class="k" style="font-weight: 600;">break</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="227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -227,16 +209,37 @@ public class GiToTaxid {</td>
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<td class="old_line diff-line-num" data-linenumber="227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
227
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<td class="new_line diff-line-num" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
209
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC209" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">getID</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">){</span><span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">getID</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">,</span> <span class="sc" style="color: #d14;">'|'</span><span class="o" style="font-weight: 600;">);}</span></span>
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<td class="old_line diff-line-num" data-linenumber="228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
228
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<td class="new_line diff-line-num" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
210
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC210" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/** Get the taxID from a header starting with a taxID or gi number */</span></span>
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<td class="old_line diff-line-num" data-linenumber="229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
229
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<td class="new_line diff-line-num" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
211
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC211" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">getID</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">delimiter</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="old_line diff-line-num old" data-linenumber="230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
230
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<td class="new_line diff-line-num old" data-linenumber="212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC230" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right deletion" style="background-color: #fac5cd;">int</span></span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">parseGiNumber</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">delimiter</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
231
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<td class="new_line diff-line-num old" data-linenumber="212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC231" 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;">x</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="n" style="color: #333;"><span class="idiff left deletion" style="background-color: #fac5cd;">array</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">[</span></span><span class="n" style="color: #333;"><span class="idiff deletion" style="background-color: #fac5cd;">x</span></span><span class="o" style="font-weight: 600;"><span class="idiff right deletion" style="background-color: #fac5cd;">]</span>;}</span></span>
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<td class="old_line diff-line-num new" data-linenumber="232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
212
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC212" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right addition" style="background-color: #c7f0d2;">long</span></span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">parseGiNumber</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">delimiter</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
213
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC213" 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;">x</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="n" style="color: #333;"><span class="idiff left addition" style="background-color: #c7f0d2;">getID</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">(</span></span><span class="n" style="color: #333;"><span class="idiff addition" style="background-color: #c7f0d2;">x</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">,</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="kc" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">true</span></span><span class="o" style="font-weight: 600;"><span class="idiff right addition" style="background-color: #c7f0d2;">)</span>;}</span></span>
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<td class="old_line diff-line-num" data-linenumber="232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
232
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<td class="new_line diff-line-num" data-linenumber="214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
214
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC214" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="nf" style="color: #900; font-weight: 600;">parseNcbiNumber</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">delimiter</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
233
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<td class="new_line diff-line-num" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
215
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC215" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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234
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<td class="new_line diff-line-num" data-linenumber="216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
216
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC216" class="line" lang="java"> </span>
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235
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<td class="new_line diff-line-num old" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC235" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/** Get the taxID from a gi number */</span></span>
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<td class="old_line diff-line-num old" data-linenumber="236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
236
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<td class="new_line diff-line-num old" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC236" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">getID</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;">gi</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="old_line diff-line-num old" data-linenumber="237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
237
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<td class="new_line diff-line-num old" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC237" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">gi</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;">gi</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="238" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
238
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<td class="new_line diff-line-num old" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC238" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">gi</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">array</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;">gi</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;">array</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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<td class="old_line diff-line-num old" data-linenumber="239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
239
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<td class="new_line diff-line-num old" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC239" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">array</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">gi</span><span class="o" style="font-weight: 600;">];</span></span>
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<td class="old_line diff-line-num new" data-linenumber="240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
217
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC217" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/** Get the taxID from a gi number;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
218
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC218" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * -1 if not present or invalid (negative input),</span></span>
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<td class="old_line diff-line-num new" data-linenumber="240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
219
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC219" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * -2 if out of range (too high) */</span></span>
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<td class="old_line diff-line-num new" data-linenumber="240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
220
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC220" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">getID</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">gi</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
221
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC221" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="nf" style="color: #900; font-weight: 600;">getID</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">gi</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
222
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC222" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
223
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC223" class="line" lang="java"> </span>
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<td class="old_line diff-line-num new" data-linenumber="240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
224
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC224" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/** Get the taxID from a gi number;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
225
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC225" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * 0 if not present,</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
226
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC226" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * -1 if invalid (negative input),</span></span>
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<td class="new_line diff-line-num new" data-linenumber="227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
227
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC227" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * -2 if out of range (too high) */</span></span>
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<td class="new_line diff-line-num new" data-linenumber="228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
228
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC228" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">getID</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">gi</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">assertInRange</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
229
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC229" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">initialized</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"To use gi numbers, you must load a gi table."</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
230
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC230" 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;">gi</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;">gi</span><span class="o" style="font-weight: 600;">></span><span class="n" style="color: #333;">maxGiLoaded</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="old_line diff-line-num new" data-linenumber="240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
231
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC231" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">assertInRange</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">gi</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;">"gi number "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">gi</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" is invalid."</span> <span class="o" style="font-weight: 600;">:</span> </span>
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<td class="old_line diff-line-num new" data-linenumber="240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
232
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC232" class="line" lang="java"> <span class="s" style="color: #d14;">"The gi number "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">gi</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" is too big: Max loaded gi number is "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">maxGiLoaded</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".\n"</span></span>
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<td class="old_line diff-line-num new" data-linenumber="240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
233
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC233" class="line" lang="java"> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"Please update the gi table with the latest version from NCBI"</span></span>
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<td class="old_line diff-line-num new" data-linenumber="240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
234
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC234" class="line" lang="java"> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" as per the instructions in gitable.sh.\n"</span></span>
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<td class="old_line diff-line-num new" data-linenumber="240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="235" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
235
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC235" class="line" lang="java"> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"To ignore this problem, please run with the -da flag.\n"</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
236
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC236" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">gi</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;">1</span> <span class="o" style="font-weight: 600;">:</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
237
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC237" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="old_line diff-line-num new" data-linenumber="240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="238" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
238
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC238" class="line" lang="java"> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">upper</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">gi</span><span class="o" style="font-weight: 600;">>>></span><span class="no" style="color: #008080;">SHIFT</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
239
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC239" class="line" lang="java"> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">lower</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;">gi</span><span class="o" style="font-weight: 600;">&</span><span class="no" style="color: #008080;">LOWERMASK</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
240
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC240" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">upper</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">Shared</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">MAX_ARRAY_LEN</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">upper</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">array</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;">gi</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;">upper</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;">array</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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<td class="old_line diff-line-num new" data-linenumber="240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
241
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC241" class="line" lang="java"> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">slice</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">array</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;">upper</span><span class="o" style="font-weight: 600;">];</span></span>
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<td class="new_line diff-line-num new" data-linenumber="242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
242
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC242" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">slice</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;">slice</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;">lower</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;">slice</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">lower</span><span class="o" style="font-weight: 600;">];</span></span>
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240
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<td class="new_line diff-line-num" data-linenumber="243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
243
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC243" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC244" class="line" lang="java"> </span>
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242
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245
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC245" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">initialize</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;">fname</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="245" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -245,8 +248,19 @@ public class GiToTaxid {</td>
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<td class="old_line diff-line-num" data-linenumber="245" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
245
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<td class="new_line diff-line-num" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
248
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC248" class="line" lang="java"> <span class="kd" style="font-weight: 600;">synchronized</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">GiToTaxid</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">class</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="old_line diff-line-num" data-linenumber="246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
246
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<td class="new_line diff-line-num" data-linenumber="249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
249
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC249" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">initialized</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">fileString</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;">fileString</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fname</span><span class="o" style="font-weight: 600;">)){</span></span>
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<td class="old_line diff-line-num" data-linenumber="247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
247
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<td class="new_line diff-line-num" data-linenumber="250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
250
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC250" class="line" lang="java"> <span class="n" style="color: #333;">fileString</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">fname</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
248
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<td class="new_line diff-line-num old" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC248" 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;">fname</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;">".int1d"</span><span class="o" style="font-weight: 600;">)){</span></span>
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<td class="old_line diff-line-num old" data-linenumber="249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
249
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<td class="new_line diff-line-num old" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC249" class="line" lang="java"> <span class="n" style="color: #333;">array</span><span class="o" style="font-weight: 600;">=</span><span class="nc" style="color: #458; font-weight: 600;">ReadWrite</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">read</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="na" style="color: #008080;">class</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">fname</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
251
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC251" 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;">fname</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;">".int2d"</span><span class="o" style="font-weight: 600;">)){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
252
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC252" class="line" lang="java"> <span class="n" style="color: #333;">array</span><span class="o" style="font-weight: 600;">=</span><span class="nc" style="color: #458; font-weight: 600;">ReadWrite</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">read</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="na" style="color: #008080;">class</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">fname</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
253
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC253" class="line" lang="java"> <span class="n" style="color: #333;">maxGiLoaded</span><span class="o" style="font-weight: 600;">=-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
254
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC254" 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;">array</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;">array</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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<td class="new_line diff-line-num new" data-linenumber="255" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
255
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC255" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">upper</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">array</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>
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<td class="new_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
256
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC256" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">section</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">array</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">upper</span><span class="o" style="font-weight: 600;">];</span></span>
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<td class="new_line diff-line-num new" data-linenumber="257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
257
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC257" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">lower</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">section</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>
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258
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC258" class="line" lang="java"> <span class="n" style="color: #333;">maxGiLoaded</span><span class="o" style="font-weight: 600;">=(((</span><span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">)</span><span class="n" style="color: #333;">upper</span><span class="o" style="font-weight: 600;">)<<</span><span class="no" style="color: #008080;">SHIFT</span><span class="o" style="font-weight: 600;">)|</span><span class="n" style="color: #333;">lower</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
259
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC259" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="260" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
260
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC260" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span><span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fname</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;">".int1d"</span><span class="o" style="font-weight: 600;">)){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
261
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC261" 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;">RuntimeException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Old gi table format filename "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">fname</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".\n"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
262
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC262" class="line" lang="java"> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"Current files should end in .int2d."</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
263
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC263" class="line" lang="java"> </span>
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250
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<td class="new_line diff-line-num" data-linenumber="264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
264
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC264" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span><span class="k" style="font-weight: 600;">else</span><span class="o" style="font-weight: 600;">{</span></span>
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251
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<td class="new_line diff-line-num" data-linenumber="265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
265
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC265" class="line" lang="java"> <span class="n" style="color: #333;">array</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">makeArray</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fname</span><span class="o" style="font-weight: 600;">);</span></span>
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252
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266
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC266" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -259,17 +273,19 @@ public class GiToTaxid {</td>
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259
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<td class="new_line diff-line-num" data-linenumber="273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
273
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC273" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">isInitialized</span><span class="o" style="font-weight: 600;">(){</span><span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">initialized</span><span class="o" style="font-weight: 600;">;}</span></span>
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260
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<td class="new_line diff-line-num" data-linenumber="274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
274
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC274" class="line" lang="java"> </span>
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<td class="old_line diff-line-num" data-linenumber="261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
261
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<td class="new_line diff-line-num" data-linenumber="275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
275
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC275" 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;">synchronized</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">unload</span><span class="o" style="font-weight: 600;">(){</span></span>
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<td class="old_line diff-line-num new" data-linenumber="262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
276
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC276" class="line" lang="java"> <span class="n" style="color: #333;">maxGiLoaded</span><span class="o" style="font-weight: 600;">=-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
262
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<td class="new_line diff-line-num" data-linenumber="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
277
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC277" class="line" lang="java"> <span class="n" style="color: #333;">array</span><span class="o" style="font-weight: 600;">=</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
263
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<td class="new_line diff-line-num" data-linenumber="278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
278
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC278" class="line" lang="java"> <span class="n" style="color: #333;">fileString</span><span class="o" style="font-weight: 600;">=</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
264
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<td class="new_line diff-line-num" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
279
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC279" class="line" lang="java"> <span class="n" style="color: #333;">initialized</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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265
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<td class="new_line diff-line-num" data-linenumber="280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
280
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC280" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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266
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281
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC281" class="line" lang="java"> </span>
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<td class="old_line diff-line-num old" data-linenumber="267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
267
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<td class="new_line diff-line-num old" data-linenumber="282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC267" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="nf" style="color: #900; font-weight: 600;">makeArray</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;">fnames</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="old_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
282
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC282" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]<span class="idiff left right addition" style="background-color: #c7f0d2;">[]</span></span> <span class="nf" style="color: #900; font-weight: 600;">makeArray</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;">fnames</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="old_line diff-line-num" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
268
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<td class="new_line diff-line-num" data-linenumber="283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
283
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC283" 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;">split</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
269
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<td class="new_line diff-line-num" data-linenumber="284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
284
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC284" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">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;">fnames</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;">split</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="n" style="color: #333;">fnames</span><span class="o" style="font-weight: 600;">};}</span></span>
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<td class="old_line diff-line-num" data-linenumber="270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
270
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<td class="new_line diff-line-num" data-linenumber="285" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
285
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC285" 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;">fnames</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">indexOf</span><span class="o" style="font-weight: 600;">(</span><span class="sc" style="color: #d14;">','</span><span class="o" style="font-weight: 600;">)>=</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">){</span><span class="n" style="color: #333;">split</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">fnames</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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<td class="old_line diff-line-num" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
271
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<td class="new_line diff-line-num" data-linenumber="286" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
286
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC286" 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;">fnames</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">indexOf</span><span class="o" style="font-weight: 600;">(</span><span class="sc" style="color: #d14;">'#'</span><span class="o" style="font-weight: 600;">)>=</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="old_line diff-line-num old" data-linenumber="272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
272
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<td class="new_line diff-line-num old" data-linenumber="287" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC272" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fnames</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">indexOf</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="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"Note: Wildcard # only works for relative paths in present working directory."</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="287" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
287
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC287" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fnames</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">indexOf</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="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"Note: Wildcard # only works for "</span></span>
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<td class="old_line diff-line-num new" data-linenumber="273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="288" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
288
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC288" class="line" lang="java"> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"relative paths in present working directory."</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
273
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<td class="new_line diff-line-num" data-linenumber="289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
289
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC289" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">File</span> <span class="n" style="color: #333;">dir</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;">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;">"user.dir"</span><span class="o" style="font-weight: 600;">));</span></span>
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<td class="old_line diff-line-num" data-linenumber="274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
274
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<td class="new_line diff-line-num" data-linenumber="290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
290
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC290" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">prefix</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">fnames</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">substring</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;">fnames</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">indexOf</span><span class="o" style="font-weight: 600;">(</span><span class="sc" style="color: #d14;">'#'</span><span class="o" style="font-weight: 600;">));</span></span>
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<td class="old_line diff-line-num" data-linenumber="275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
275
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<td class="new_line diff-line-num" data-linenumber="291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
291
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC291" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">suffix</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">fnames</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">substring</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fnames</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">indexOf</span><span class="o" style="font-weight: 600;">(</span><span class="sc" style="color: #d14;">'#'</span><span class="o" style="font-weight: 600;">)+</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -290,20 +306,28 @@ public class GiToTaxid {</td>
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<td class="old_line diff-line-num" data-linenumber="290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
290
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<td class="new_line diff-line-num" data-linenumber="306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
306
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC306" 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;">RuntimeException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Invalid file: "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">fnames</span><span class="o" style="font-weight: 600;">);</span></span>
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291
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307
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC307" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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292
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<td class="new_line diff-line-num" data-linenumber="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
308
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC308" class="line" lang="java"> </span>
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<td class="old_line diff-line-num old" data-linenumber="293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
293
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<td class="new_line diff-line-num old" data-linenumber="309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC293" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">IntList</span> <span class="n" style="color: #333;">list</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;">IntList</span><span class="o" style="font-weight: 600;">();</span></span>
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<td class="old_line diff-line-num old" data-linenumber="294" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
294
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<td class="new_line diff-line-num old" data-linenumber="309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC294" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// assert(max<Integer.MAX_VALUE) : "Overflow.";</span></span>
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<td class="old_line diff-line-num old" data-linenumber="295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
295
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<td class="new_line diff-line-num old" data-linenumber="309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC295" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// int[] x=new int[(int)max+1];</span></span>
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<td class="old_line diff-line-num old" data-linenumber="296" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
296
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<td class="new_line diff-line-num old" data-linenumber="309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC296" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// Arrays.fill(x, -1);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
309
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC309" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numLists</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">32</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
310
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC310" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">IntList</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">lists</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;">IntList</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">numLists</span><span class="o" style="font-weight: 600;">];</span></span>
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297
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<td class="new_line diff-line-num" data-linenumber="311" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
311
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC311" class="line" lang="java"> </span>
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<td class="old_line diff-line-num" data-linenumber="298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
298
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<td class="new_line diff-line-num" data-linenumber="312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
312
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC312" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">long</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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<td class="old_line diff-line-num" data-linenumber="299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
299
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<td class="new_line diff-line-num" data-linenumber="313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
313
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC313" 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;">s</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">split</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="old_line diff-line-num old" data-linenumber="300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
300
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<td class="new_line diff-line-num old" data-linenumber="314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC300" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">count</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">addToList</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">list</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
314
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC314" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">count</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">addToList</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">list<span class="idiff left right addition" style="background-color: #c7f0d2;">s</span></span><span class="o" style="font-weight: 600;">);</span></span>
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301
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<td class="new_line diff-line-num" data-linenumber="315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
315
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC315" 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;">count</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
302
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<td class="new_line diff-line-num" data-linenumber="316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
316
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC316" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="old_line diff-line-num old" data-linenumber="303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
303
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<td class="new_line diff-line-num old" data-linenumber="317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC303" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">list</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">shrink</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">array</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
317
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC317" 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;">lists</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>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
318
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<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;">lists</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="kc" style="font-weight: 600;">null</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">lists</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;">size</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="new_line diff-line-num new" data-linenumber="319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
319
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC319" class="line" lang="java"> <span class="n" style="color: #333;">lists</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;">shrink</span><span class="o" style="font-weight: 600;">();</span></span>
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<td class="new_line diff-line-num new" data-linenumber="320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
320
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC320" class="line" lang="java"> <span class="n" style="color: #333;">numLists</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>
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<td class="new_line diff-line-num new" data-linenumber="321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
321
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC321" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
322
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC322" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
323
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC323" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[][]</span> <span class="n" style="color: #333;">table</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;">numLists</span><span class="o" style="font-weight: 600;">][];</span></span>
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<td class="new_line diff-line-num new" data-linenumber="324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
324
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC324" 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;">numLists</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++){</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
325
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC325" class="line" lang="java"> <span class="n" style="color: #333;">table</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;">lists</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;">array</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
326
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC326" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
327
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC327" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">table</span><span class="o" style="font-weight: 600;">;</span></span>
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304
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<td class="new_line diff-line-num" data-linenumber="328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
328
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC328" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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305
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<td class="new_line diff-line-num" data-linenumber="329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
329
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC329" class="line" lang="java"> </span>
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<td class="old_line diff-line-num old" data-linenumber="306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
306
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<td class="new_line diff-line-num old" data-linenumber="330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC306" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="nf" style="color: #900; font-weight: 600;">addToList</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;">fname</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">IntList</span> <span class="n" style="color: #333;">list</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="old_line diff-line-num new" data-linenumber="307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
330
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC330" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="nf" style="color: #900; font-weight: 600;">addToList</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;">fname</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">IntList</span><span class="o" style="font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">[]</span></span> <span class="n" style="color: #333;">list<span class="idiff right addition" style="background-color: #c7f0d2;">s</span></span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="old_line diff-line-num" data-linenumber="307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
307
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<td class="new_line diff-line-num" data-linenumber="331" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
331
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC331" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">warned</span><span class="o" style="font-weight: 600;">=</span><span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
308
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<td class="new_line diff-line-num" data-linenumber="332" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
332
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC332" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">ByteFile</span> <span class="n" style="color: #333;">bf</span><span class="o" style="font-weight: 600;">=</span><span class="nc" style="color: #458; font-weight: 600;">ByteFile</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">makeByteFile</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fname</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
309
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<td class="new_line diff-line-num" data-linenumber="333" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
333
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC333" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">long</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="n" style="color: #333;">invalid</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="340" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -316,34 +340,18 @@ public class GiToTaxid {</td>
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<td class="old_line diff-line-num" data-linenumber="316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
316
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<td class="new_line diff-line-num" data-linenumber="340" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
340
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC340" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">tab2</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;">tab2</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">tab3</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">tab3</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #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;">tab2</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;">tab3</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;">line</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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<td class="old_line diff-line-num" data-linenumber="317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
317
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<td class="new_line diff-line-num" data-linenumber="341" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
341
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC341" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">tab2</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">tab2</span><span class="o" style="font-weight: 600;">]==</span><span class="sc" style="color: #d14;">'\t'</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">tab2</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;">tab3</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">", '"</span><span class="o" style="font-weight: 600;">+</span><span class="k" style="font-weight: 600;">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;">line</span><span class="o" style="font-weight: 600;">)+</span><span class="s" style="color: #d14;">"'"</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
318
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<td class="new_line diff-line-num" data-linenumber="342" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
342
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC342" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">tab3</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">tab3</span><span class="o" style="font-weight: 600;">]==</span><span class="sc" style="color: #d14;">'\t'</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">tab2</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;">tab3</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">", '"</span><span class="o" style="font-weight: 600;">+</span><span class="k" style="font-weight: 600;">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;">line</span><span class="o" style="font-weight: 600;">)+</span><span class="s" style="color: #d14;">"'"</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
319
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<td class="new_line diff-line-num old" data-linenumber="343" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC319" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right deletion" style="background-color: #fac5cd;">//</span> assert(false) : tab2+", "+tab3+", '"+new String(line)+"'";</span></span>
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<td class="old_line diff-line-num new" data-linenumber="320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="343" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
343
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC343" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right addition" style="background-color: #c7f0d2;">//</span>assert(false) : tab2+", "+tab3+", '"+new String(line)+"'";</span></span>
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<td class="old_line diff-line-num" data-linenumber="320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
320
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<td class="new_line diff-line-num" data-linenumber="344" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
344
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC344" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tid</span><span class="o" style="font-weight: 600;">=</span><span class="nc" style="color: #458; font-weight: 600;">Parse</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;">line</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">tab2</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;">tab3</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
321
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<td class="new_line diff-line-num" data-linenumber="345" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
345
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC345" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">gi</span><span class="o" style="font-weight: 600;">=</span><span class="nc" style="color: #458; font-weight: 600;">Parse</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;">line</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">tab3</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;">line</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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<td class="old_line diff-line-num old" data-linenumber="322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
322
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<td class="new_line diff-line-num old" data-linenumber="346" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC322" 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;">gi</span><span class="o" style="font-weight: 600;"><span class="idiff left deletion" style="background-color: #fac5cd;">>=</span></span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">Shared</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">.</span></span><span class="na" style="color: #008080;"><span class="idiff deletion" style="background-color: #fac5cd;">MAX_ARRAY_LEN</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">||</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333;"><span class="idiff deletion" style="background-color: #fac5cd;">gi</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;"><</span></span><span class="mi" style="color: #099;"><span class="idiff deletion" style="background-color: #fac5cd;">0</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">){</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right deletion" style="background-color: #fac5cd;">//A gi over 2.5b was observed May 3, 2021.</span></span></span>
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<td class="old_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="346" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
346
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC346" 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;">gi</span><span class="o" style="font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;"><</span></span><span class="mi" style="color: #099;"><span class="idiff addition" style="background-color: #c7f0d2;">0</span></span><span class="o" style="font-weight: 600;"><span class="idiff right addition" style="background-color: #c7f0d2;">){</span></span></span>
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323
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<td class="new_line diff-line-num" data-linenumber="347" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
347
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC347" class="line" lang="java"> <span class="n" style="color: #333;">invalid</span><span class="o" style="font-weight: 600;">++;</span></span>
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<td class="old_line diff-line-num" data-linenumber="324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
324
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<td class="new_line diff-line-num" data-linenumber="348" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
348
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC348" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span><span class="k" style="font-weight: 600;">else</span><span class="o" style="font-weight: 600;">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
325
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<td class="new_line diff-line-num old" data-linenumber="349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC325" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">gi</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="s" style="color: #d14;">"tid="</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">tid</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">", gi="</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">gi</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">", line=\n'"</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;">line</span><span class="o" style="font-weight: 600;">)+</span><span class="s" style="color: #d14;">"'"</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
326
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<td class="new_line diff-line-num old" data-linenumber="349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC326" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">old</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">list</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;">gi</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
327
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<td class="new_line diff-line-num old" data-linenumber="349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC327" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">old</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;">old</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">tid</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"Contradictory entries for gi "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">gi</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;">old</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;">tid</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"\n'"</span><span class="o" style="font-weight: 600;">+</span><span class="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;">line</span><span class="o" style="font-weight: 600;">)+</span><span class="s" style="color: #d14;">"'\ntab2="</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">tab2</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">", tab3="</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">tab3</span><span class="o" style="font-weight: 600;">;</span></span>
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328
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<td class="new_line diff-line-num old" data-linenumber="349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC328" class="line" lang="java"> </span>
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<td class="old_line diff-line-num old" data-linenumber="329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
329
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<td class="new_line diff-line-num old" data-linenumber="349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC329" class="line" lang="java"> <span class="n" style="color: #333;">list</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">set</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">gi</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">tid</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
330
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<td class="new_line diff-line-num old" data-linenumber="349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC330" class="line" lang="java"> </span>
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<td class="old_line diff-line-num old" data-linenumber="331" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
331
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<td class="new_line diff-line-num old" data-linenumber="349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC331" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//assert(x[gi]==-1 || x[gi]==ncbi) : "Contradictory entries for gi "+gi+": "+x[gi]+" -> "+ncbi;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="332" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
332
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<td class="new_line diff-line-num old" data-linenumber="349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC332" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// if(x[gi]!=-1 && x[gi]!=ncbi){</span></span>
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<td class="old_line diff-line-num old" data-linenumber="333" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
333
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<td class="new_line diff-line-num old" data-linenumber="349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC333" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// if(!warned){</span></span>
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<td class="old_line diff-line-num old" data-linenumber="334" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
334
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<td class="new_line diff-line-num old" data-linenumber="349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC334" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// System.err.println("***WARNING*** For file "+fname+":\n"+</span></span>
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<td class="old_line diff-line-num old" data-linenumber="335" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
335
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<td class="new_line diff-line-num old" data-linenumber="349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC335" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// ("Contradictory entries for gi "+gi+": mapped to both taxID "+x[gi]+" and taxID "+ncbi)+</span></span>
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<td class="old_line diff-line-num old" data-linenumber="336" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
336
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<td class="new_line diff-line-num old" data-linenumber="349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC336" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// "\nThis may be an error from NCBI and you may wish to report it, but it is\n"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="337" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
337
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<td class="new_line diff-line-num old" data-linenumber="349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC337" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// + "being suppressed because NCBI data is known to contain multi-mapped gi numbers,\n"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="338" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
338
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<td class="new_line diff-line-num old" data-linenumber="349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC338" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// + "at least between nucleotide and protein, and gi numbers are deprecated anyway.");</span></span>
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<td class="old_line diff-line-num old" data-linenumber="339" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
339
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<td class="new_line diff-line-num old" data-linenumber="349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC339" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// warned=true;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="340" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
340
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<td class="new_line diff-line-num old" data-linenumber="349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC340" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// }</span></span>
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341
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<td class="new_line diff-line-num old" data-linenumber="349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC341" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// }else{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="342" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
342
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<td class="new_line diff-line-num old" data-linenumber="349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC342" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// x[gi]=ncbi;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="343" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
343
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<td class="new_line diff-line-num old" data-linenumber="349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC343" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// }</span></span>
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<td class="old_line diff-line-num new" data-linenumber="344" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
349
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC349" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">gi</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="s" style="color: #d14;">"tid="</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">tid</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">", gi="</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">gi</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">", line=\n'"</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;">line</span><span class="o" style="font-weight: 600;">)+</span><span class="s" style="color: #d14;">"'"</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="344" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="350" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
350
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC350" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">old</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">setID</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">gi</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">tid</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">lists</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="344" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="351" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
351
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC351" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">old</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;">old</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">tid</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"Contradictory entries for gi "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">gi</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;">old</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;">tid</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"\n'"</span><span class="o" style="font-weight: 600;">+</span><span class="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;">line</span><span class="o" style="font-weight: 600;">)+</span><span class="s" style="color: #d14;">"'\ntab2="</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">tab2</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">", tab3="</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">tab3</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="344" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
344
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<td class="new_line diff-line-num" data-linenumber="352" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
352
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC352" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="345" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
345
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<td class="new_line diff-line-num" data-linenumber="353" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
353
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC353" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span><span class="k" style="font-weight: 600;">else</span><span class="o" style="font-weight: 600;">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="346" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
346
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<td class="new_line diff-line-num old" data-linenumber="354" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC346" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="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="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="n" style="color: #333;">fname</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;">count</span><span class="o" style="font-weight: 600;">);}</span><span class="c1" style="color: #998; font-style: italic;">//debug</span></span>
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<td class="new_line diff-line-num new" data-linenumber="354" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
354
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC354" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right addition" style="background-color: #c7f0d2;">//</span>if(line.length==0){System.err.println(fname+", "+count);}//debug</span></span>
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347
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<td class="new_line diff-line-num" data-linenumber="355" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
355
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC355" class="line" lang="java"> <span class="n" style="color: #333;">invalid</span><span class="o" style="font-weight: 600;">++;</span></span>
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348
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<td class="new_line diff-line-num" data-linenumber="356" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
356
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC356" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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349
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<td class="new_line diff-line-num" data-linenumber="357" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
357
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC357" class="line" lang="java"> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">bf</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextLine</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="353" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="361" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -353,6 +361,28 @@ public class GiToTaxid {</td>
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<td class="old_line diff-line-num" data-linenumber="353" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
353
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<td class="new_line diff-line-num" data-linenumber="361" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
361
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC361" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">count</span><span class="o" style="font-weight: 600;">;</span></span>
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354
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<td class="new_line diff-line-num" data-linenumber="362" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
362
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC362" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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355
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<td class="new_line diff-line-num" data-linenumber="363" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
363
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC363" class="line" lang="java"> </span>
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<td class="old_line diff-line-num new" data-linenumber="356" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="364" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
364
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC364" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">getID</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">gi</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">IntList</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">lists</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="old_line diff-line-num new" data-linenumber="356" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="365" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
365
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC365" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">gi</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="s" style="color: #d14;">"gi number "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">gi</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" is invalid."</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="356" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="366" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
366
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC366" class="line" lang="java"> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">upper</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">gi</span><span class="o" style="font-weight: 600;">>>></span><span class="no" style="color: #008080;">SHIFT</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="356" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
367
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC367" class="line" lang="java"> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">lower</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;">gi</span><span class="o" style="font-weight: 600;">&</span><span class="no" style="color: #008080;">LOWERMASK</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="356" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="368" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
368
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC368" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">upper</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">Shared</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">MAX_ARRAY_LEN</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">gi</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;">upper</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="356" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="369" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
369
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC369" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">IntList</span> <span class="n" style="color: #333;">list</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">lists</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;">upper</span><span class="o" style="font-weight: 600;">];</span></span>
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<td class="old_line diff-line-num new" data-linenumber="356" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="370" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
370
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC370" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">lower</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;">1</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">lower</span><span class="o" style="font-weight: 600;">>=</span><span class="n" style="color: #333;">list</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;">2</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">list</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;">lower</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="371" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
371
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC371" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="372" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
372
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC372" class="line" lang="java"> </span>
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<td class="old_line diff-line-num new" data-linenumber="356" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="373" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
373
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC373" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">setID</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">gi</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;">tid</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">IntList</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">lists</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="old_line diff-line-num new" data-linenumber="356" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="374" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
374
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC374" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">gi</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="s" style="color: #d14;">"gi number "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">gi</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" is invalid."</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="356" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="375" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
375
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC375" class="line" lang="java"> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">upper</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">gi</span><span class="o" style="font-weight: 600;">>>></span><span class="no" style="color: #008080;">SHIFT</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="356" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="376" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
376
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC376" class="line" lang="java"> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">lower</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;">gi</span><span class="o" style="font-weight: 600;">&</span><span class="no" style="color: #008080;">LOWERMASK</span><span class="o" style="font-weight: 600;">);</span></span>
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377
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC377" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">upper</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">Shared</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">MAX_ARRAY_LEN</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">gi</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;">upper</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="378" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
378
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC378" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">IntList</span> <span class="n" style="color: #333;">list</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">lists</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;">upper</span><span class="o" style="font-weight: 600;">];</span></span>
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<td class="old_line diff-line-num new" data-linenumber="356" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="379" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
379
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC379" 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;">list</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;">list</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">lists</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;">upper</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;">IntList</span><span class="o" style="font-weight: 600;">();}</span></span>
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<td class="old_line diff-line-num new" data-linenumber="356" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
380
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC380" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">old</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">lower</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;">1</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">lower</span><span class="o" style="font-weight: 600;">>=</span><span class="n" style="color: #333;">list</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;">2</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">list</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;">lower</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
381
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC381" class="line" lang="java"> <span class="n" style="color: #333;">list</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">set</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">lower</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">tid</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="382" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
382
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC382" class="line" lang="java"> <span class="n" style="color: #333;">maxGiLoaded</span><span class="o" style="font-weight: 600;">=</span><span class="nc" style="color: #458; font-weight: 600;">Tools</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">max</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">gi</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">maxGiLoaded</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
383
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC383" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">old</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
384
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC384" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
385
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC385" class="line" lang="java"> </span>
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<td class="old_line diff-line-num" data-linenumber="356" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
356
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<td class="new_line diff-line-num" data-linenumber="386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
386
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC386" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// private static int[] makeArrayOld(String fnames){</span></span>
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357
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<td class="new_line diff-line-num" data-linenumber="387" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
387
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC387" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// String[] split;</span></span>
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358
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<td class="new_line diff-line-num" data-linenumber="388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
388
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC388" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// if(new File(fnames).exists()){split=new String[] {fnames};}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="420" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="450" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -420,7 +450,12 @@ public class GiToTaxid {</td>
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<td class="old_line diff-line-num" data-linenumber="420" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
420
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<td class="new_line diff-line-num" data-linenumber="450" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
450
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC450" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// return count;</span></span>
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421
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<td class="new_line diff-line-num" data-linenumber="451" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
451
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC451" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// }</span></span>
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422
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<td class="new_line diff-line-num" data-linenumber="452" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
452
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC452" class="line" lang="java"> </span>
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<td class="old_line diff-line-num old" data-linenumber="423" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
423
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<td class="new_line diff-line-num old" data-linenumber="453" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC423" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">array</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="453" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
453
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC453" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">maxGiLoaded</span><span class="o" style="font-weight: 600;">=-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="454" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
454
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC454" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[][]</span> <span class="n" style="color: #333;">array</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="455" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
455
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC455" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="no" style="color: #008080;">SHIFT</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">30</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="456" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
456
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC456" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="no" style="color: #008080;">UPPERMASK</span><span class="o" style="font-weight: 600;">=(-</span><span class="mi" style="color: #099;">1L</span><span class="o" style="font-weight: 600;">)<<</span><span class="no" style="color: #008080;">SHIFT</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="457" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
457
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC457" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="no" style="color: #008080;">LOWERMASK</span><span class="o" style="font-weight: 600;">=~</span><span class="no" style="color: #008080;">UPPERMASK</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="458" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
458
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC458" class="line" lang="java"> </span>
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424
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<td class="new_line diff-line-num" data-linenumber="459" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
459
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC459" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">fileString</span><span class="o" style="font-weight: 600;">;</span></span>
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425
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460
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC460" class="line" lang="java"> </span>
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<td class="old_line diff-line-num" data-linenumber="426" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
426
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<td class="new_line diff-line-num" data-linenumber="461" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
461
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC461" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">verbose</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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<a href="https://salsa.debian.org/med-team/bbmap/-/commit/1c662261847da712e5b04b94277f8aa712c37619#901bdbfa60205c675be60d3fa183dbbff4f5658b" style="color: #1068bf; text-decoration: none;"><strong style="font-weight: bold;">current/tax/GiToTaxidInt.java</strong></a>
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<td class="new_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1" class="line" lang="java"><span class="kn" style="font-weight: 600;">package</span> <span class="nn" style="color: #555;">tax</span><span class="o" style="font-weight: 600;">;</span></span>
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2
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC2" class="line" lang="java"></span>
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<td class="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3" 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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<td class="new_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
4
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC4" 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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5
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC5" class="line" lang="java"></span>
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<td class="new_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
6
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC6" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">fileIO.ByteFile</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
7
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC7" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">fileIO.ReadWrite</span><span class="o" style="font-weight: 600;">;</span></span>
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8
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC8" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">shared.Parse</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC9" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">shared.Shared</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC10" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">shared.Tools</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC11" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">structures.IntList</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC12" class="line" lang="java"></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC13" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<td class="new_line diff-line-num new" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC14" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @author Brian Bushnell</span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC15" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @date Mar 10, 2015</span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC16" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC17" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<td class="new_line diff-line-num new" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
18
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC18" 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;">GiToTaxidInt</span> <span class="o" style="font-weight: 600;">{</span></span>
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19
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC19" class="line" lang="java"> </span>
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<td class="new_line diff-line-num new" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
20
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC20" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">main</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;">args</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
21
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC21" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">ReadWrite</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">USE_UNPIGZ</span><span class="o" style="font-weight: 600;">=</span><span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
22
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC22" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">ReadWrite</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">USE_PIGZ</span><span class="o" style="font-weight: 600;">=</span><span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
23
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC23" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">ReadWrite</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">ZIPLEVEL</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">9</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
24
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC24" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">ReadWrite</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">PIGZ_BLOCKSIZE</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">256</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
25
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC25" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// ReadWrite.PIGZ_ITERATIONS=30;</span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC26" class="line" lang="java"> </span>
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<td class="new_line diff-line-num new" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
27
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC27" 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;">arg</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
28
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC28" 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;">split</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">arg</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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<td class="new_line diff-line-num new" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
29
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC29" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">split</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;">toLowerCase</span><span class="o" style="font-weight: 600;">();</span></span>
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<td class="new_line diff-line-num new" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
30
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC30" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">split</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;">split</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="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
31
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC31" class="line" lang="java"> <span class="n" style="color: #333;">shared</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">Parser</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseZip</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">arg</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;">b</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
32
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC32" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
33
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC33" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// if(args.length>2 && false){//Run a test</span></span>
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<td class="new_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
34
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC34" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// test(args);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
35
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC35" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// }else </span></span>
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<td class="new_line diff-line-num new" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
36
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC36" 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;">args</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;">2</span><span class="o" style="font-weight: 600;">){</span><span class="c1" style="color: #998; font-style: italic;">//Write array</span></span>
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<td class="new_line diff-line-num new" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
37
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC37" class="line" lang="java"> <span class="n" style="color: #333;">initialize</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">]);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
38
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC38" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">ReadWrite</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">write</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">array</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">1</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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39
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC39" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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40
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC40" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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41
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC41" class="line" lang="java"> </span>
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<td class="new_line diff-line-num new" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
42
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<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="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">test</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;">args</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
43
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC43" 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="n" style="color: #333;">getID</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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<td class="new_line diff-line-num new" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
44
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC44" 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="n" style="color: #333;">getID</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">10000</span><span class="o" style="font-weight: 600;">));</span></span>
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<td class="new_line diff-line-num new" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
45
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC45" 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="n" style="color: #333;">getID</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">10001</span><span class="o" style="font-weight: 600;">));</span></span>
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<td class="new_line diff-line-num new" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
46
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC46" 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="n" style="color: #333;">getID</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">10002</span><span class="o" style="font-weight: 600;">));</span></span>
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<td class="new_line diff-line-num new" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
47
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC47" 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="n" style="color: #333;">getID</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">10003</span><span class="o" style="font-weight: 600;">));</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
48
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC48" 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="n" style="color: #333;">getID</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">10004</span><span class="o" style="font-weight: 600;">));</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
49
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC49" 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="n" style="color: #333;">getID</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">10005</span><span class="o" style="font-weight: 600;">));</span></span>
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<td class="new_line diff-line-num new" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
50
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC50" 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="n" style="color: #333;">getID</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">100000</span><span class="o" style="font-weight: 600;">));</span></span>
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<td class="new_line diff-line-num new" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
51
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC51" 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="n" style="color: #333;">getID</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">1000000</span><span class="o" style="font-weight: 600;">));</span></span>
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<td class="new_line diff-line-num new" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
52
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC52" 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="n" style="color: #333;">getID</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">10000000</span><span class="o" style="font-weight: 600;">));</span></span>
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<td class="new_line diff-line-num new" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
53
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC53" class="line" lang="java"> </span>
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<td class="new_line diff-line-num new" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
54
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC54" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">TaxTree</span> <span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">=</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
55
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC55" 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;">args</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>
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<td class="new_line diff-line-num new" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
56
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC56" class="line" lang="java"> <span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">=</span><span class="nc" style="color: #458; font-weight: 600;">TaxTree</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">loadTaxTree</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">0</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="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
57
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC57" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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58
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC58" class="line" lang="java"> </span>
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<td class="new_line diff-line-num new" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
59
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC59" 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;">"Strings:"</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
60
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC60" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
61
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC61" class="line" lang="java"> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">getID</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"gi|18104025|emb|AJ427095.1| Ceratitis capitata centromeric or pericentromeric satellite DNA, clone 44"</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
62
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC62" 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="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
63
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC63" 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;">tree</span><span class="o" style="font-weight: 600;">!=</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
64
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC64" 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="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getNode</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">));</span></span>
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<td class="new_line diff-line-num new" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
65
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC65" class="line" lang="java"> <span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">incrementRaw</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">30</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
66
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC66" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
67
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC67" class="line" lang="java"> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">getID</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"gi|15982920|gb|AY057568.1| Arabidopsis thaliana AT5g43500/MWF20_22 mRNA, complete cds"</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
68
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC68" 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="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
69
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<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;">tree</span><span class="o" style="font-weight: 600;">!=</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
70
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC70" 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="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getNode</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">));</span></span>
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<td class="new_line diff-line-num new" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
71
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC71" class="line" lang="java"> <span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">incrementRaw</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">40</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
72
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC72" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
73
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC73" class="line" lang="java"> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">getID</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"gi|481043749|gb|KC494054.1| Plesiochorus cymbiformis isolate ST05-58 internal transcribed spacer 2, partial sequence"</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
74
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<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="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
75
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC75" 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;">tree</span><span class="o" style="font-weight: 600;">!=</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
76
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC76" 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="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getNode</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">));</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
77
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC77" class="line" lang="java"> <span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">incrementRaw</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">20</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
78
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC78" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
79
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC79" class="line" lang="java"> </span>
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<td class="new_line diff-line-num new" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
80
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<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;">tree</span><span class="o" style="font-weight: 600;">!=</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
81
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC81" class="line" lang="java"> <span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">percolateUp</span><span class="o" style="font-weight: 600;">();</span></span>
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<td class="new_line diff-line-num new" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
82
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC82" class="line" lang="java"> <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;">TaxNode</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">nodes</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">gatherNodesAtLeastLimit</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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<td class="new_line diff-line-num new" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
83
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC83" 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;">TaxNode</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">nodes</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
84
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<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="n" style="color: #333;">n</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
85
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC85" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
86
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC86" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
87
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC87" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
88
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC88" class="line" lang="java"> </span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
89
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC89" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">parseGiToTaxid</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;">s</span><span class="o" style="font-weight: 600;">){</span><span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">parseGiToTaxid</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">,</span> <span class="sc" style="color: #d14;">'|'</span><span class="o" style="font-weight: 600;">);}</span></span>
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90
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC90" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">parseGiToTaxid</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;">s</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">delimiter</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
91
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC91" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">parseGiNumber</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">delimiter</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
92
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC92" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">x</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;">s</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
93
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC93" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">array</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="s" style="color: #d14;">"To use gi numbers, you must load a gi table."</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
94
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC94" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// if(x>=array.length || array[x]<0){x=(int)(Math.random()*array.length);} //Test to make sure array is nonempty.</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
95
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<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;">x</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;">x</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">array</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="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">array</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">];}</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
96
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC96" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">array</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="s" style="color: #d14;">"The GI number "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" is too big.\n"</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
97
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC97" class="line" lang="java"> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"Please update the gi table with the latest version from NCBI as per the instructions in gitable.sh.\n"</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
98
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC98" class="line" lang="java"> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"To ignore this problem, please run with the -da flag.\n"</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
99
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC99" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
100
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC100" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
101
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC101" class="line" lang="java"> </span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
102
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC102" class="line" lang="java"></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
103
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC103" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">parseGiToTaxid</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">){</span><span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">parseGiToTaxid</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">,</span> <span class="sc" style="color: #d14;">'|'</span><span class="o" style="font-weight: 600;">);}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
104
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC104" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">parseGiToTaxid</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">delimiter</span><span class="o" style="font-weight: 600;">){</span></span>
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105
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC105" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">parseGiNumber</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">delimiter</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
106
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC106" 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;">x</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;">x</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">array</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="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">array</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;">x</span><span class="o" style="font-weight: 600;">];}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
107
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC107" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">x</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 class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;}</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
108
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC108" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(</span><span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
109
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC109" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
110
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC110" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
111
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC111" class="line" lang="java"> </span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
112
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC112" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/** Parse a gi number, or return -1 if formatted incorrectly. */</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
113
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC113" class="line" lang="java"> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">parseGiNumber</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;">s</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">delimiter</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
114
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC114" 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;">s</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;">s</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="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;}</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
115
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC115" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// System.err.println("a");</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
116
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<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;">s</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">charAt</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="sc" style="color: #d14;">'>'</span><span class="o" style="font-weight: 600;">){</span><span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">getID</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">substring</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;">delimiter</span><span class="o" style="font-weight: 600;">);}</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
117
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC117" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// System.err.println("b");</span></span>
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<td class="new_line diff-line-num new" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
118
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC118" 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;">s</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;">"gi"</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 class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
119
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC119" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// System.err.println("c");</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
120
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC120" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// System.err.println("d");</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
121
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC121" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">initial</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">indexOf</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">delimiter</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
122
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC122" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// System.err.println("e");</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
123
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<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;">initial</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="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
124
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC124" 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;">delimiter</span><span class="o" style="font-weight: 600;">!=</span><span class="sc" style="color: #d14;">'~'</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
125
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC125" class="line" lang="java"> <span class="n" style="color: #333;">delimiter</span><span class="o" style="font-weight: 600;">=</span><span class="sc" style="color: #d14;">'~'</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
126
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC126" class="line" lang="java"> <span class="n" style="color: #333;">initial</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">indexOf</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">delimiter</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
127
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC127" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
128
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC128" 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;">initial</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="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
129
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC129" class="line" lang="java"> <span class="n" style="color: #333;">delimiter</span><span class="o" style="font-weight: 600;">=</span><span class="sc" style="color: #d14;">'_'</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
130
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC130" class="line" lang="java"> <span class="n" style="color: #333;">initial</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">indexOf</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">delimiter</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
131
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC131" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
132
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC132" 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;">initial</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 class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
133
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC133" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// System.err.println("f");</span></span>
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<td class="new_line diff-line-num new" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
134
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC134" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// System.err.println("g");</span></span>
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<td class="new_line diff-line-num new" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
135
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC135" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
136
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC136" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// System.err.println("h");</span></span>
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<td class="new_line diff-line-num new" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
137
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC137" 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;">Tools</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isDigit</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">charAt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">initial</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">))){</span><span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;}</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
138
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC138" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// System.err.println("i");</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
139
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC139" class="line" lang="java"> </span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
140
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC140" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">number</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="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
141
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC141" 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;">initial</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;">s</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>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
142
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC142" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">charAt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
143
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<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;">c</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">delimiter</span><span class="o" style="font-weight: 600;">){</span><span class="k" style="font-weight: 600;">break</span><span class="o" style="font-weight: 600;">;}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
144
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC144" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Tools</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isDigit</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">));</span></span>
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<td class="new_line diff-line-num new" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
145
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC145" class="line" lang="java"> <span class="n" style="color: #333;">number</span><span class="o" style="font-weight: 600;">=(</span><span class="n" style="color: #333;">number</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;">c</span><span class="o" style="font-weight: 600;">-</span><span class="sc" style="color: #d14;">'0'</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
146
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC146" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
147
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC147" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// System.err.println("j: "+number);</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
148
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC148" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">number</span><span class="o" style="font-weight: 600;">;</span></span>
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149
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC149" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
150
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC150" class="line" lang="java"> </span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
151
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC151" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/** Parse a ncbi number, or return -1 if formatted incorrectly. */</span></span>
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<td class="new_line diff-line-num new" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
152
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC152" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">parseTaxidNumber</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;">s</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">delimiter</span><span class="o" style="font-weight: 600;">){</span></span>
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153
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<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;">s</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;">s</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="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;}</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
154
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<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;">s</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">charAt</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="sc" style="color: #d14;">'>'</span><span class="o" style="font-weight: 600;">){</span><span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">parseTaxidNumber</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">substring</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;">delimiter</span><span class="o" style="font-weight: 600;">);}</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
155
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<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;">s</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;">"ncbi"</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;">s</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;">"tid"</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 class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;}</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
156
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC156" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">initial</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">indexOf</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">delimiter</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
157
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC157" 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;">initial</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="new_line diff-line-num new" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
158
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC158" class="line" lang="java"> <span class="n" style="color: #333;">delimiter</span><span class="o" style="font-weight: 600;">=</span><span class="sc" style="color: #d14;">'_'</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
159
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC159" class="line" lang="java"> <span class="n" style="color: #333;">initial</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">indexOf</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">delimiter</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
160
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC160" 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;">initial</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 class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
161
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC161" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
162
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC162" 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;">Tools</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isDigit</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">charAt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">initial</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">))){</span><span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
163
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC163" class="line" lang="java"> </span>
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<td class="new_line diff-line-num new" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
164
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC164" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">number</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="new_line diff-line-num new" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
165
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC165" 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;">initial</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;">s</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>
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<td class="new_line diff-line-num new" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
166
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC166" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">charAt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
167
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC167" 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;">c</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">delimiter</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">==</span><span class="sc" style="color: #d14;">' '</span><span class="o" style="font-weight: 600;">){</span><span class="k" style="font-weight: 600;">break</span><span class="o" style="font-weight: 600;">;}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
168
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC168" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Tools</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isDigit</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"\n"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
169
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC169" class="line" lang="java"> <span class="n" style="color: #333;">number</span><span class="o" style="font-weight: 600;">=(</span><span class="n" style="color: #333;">number</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;">c</span><span class="o" style="font-weight: 600;">-</span><span class="sc" style="color: #d14;">'0'</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
170
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC170" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
171
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC171" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">number</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
172
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC172" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
173
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC173" class="line" lang="java"> </span>
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<td class="new_line diff-line-num new" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
174
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC174" class="line" lang="java"></span>
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<td class="new_line diff-line-num new" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
175
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC175" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">getID</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;">s</span><span class="o" style="font-weight: 600;">){</span><span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">getID</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">,</span> <span class="sc" style="color: #d14;">'|'</span><span class="o" style="font-weight: 600;">);}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
176
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC176" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/** Get the taxID from a header starting with a taxID or gi number */</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
177
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC177" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">getID</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;">s</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">delimiter</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
178
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC178" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">parseTaxidNumber</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">delimiter</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
179
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC179" 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;">x</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="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">;}</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
180
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC180" class="line" lang="java"> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">parseGiNumber</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">delimiter</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
181
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<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;">x</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="n" style="color: #333;">array</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">];}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
182
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<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 class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
183
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC183" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
184
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC184" class="line" lang="java"> </span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
185
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC185" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/** Parse a gi number, or return -1 if formatted incorrectly. */</span></span>
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<td class="new_line diff-line-num new" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
186
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC186" class="line" lang="java"> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">parseGiNumber</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">delimiter</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
187
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<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;">s</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;">s</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="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
188
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC188" 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;">Tools</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="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"gi"</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="nc" style="color: #458; font-weight: 600;">Tools</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="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">">gi"</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 class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
189
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC189" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">initial</span><span class="o" style="font-weight: 600;">=</span><span class="nc" style="color: #458; font-weight: 600;">Tools</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">indexOf</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">,</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="o" style="font-weight: 600;">)</span><span class="n" style="color: #333;">delimiter</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
190
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<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;">initial</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="new_line diff-line-num new" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
191
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC191" class="line" lang="java"> <span class="n" style="color: #333;">delimiter</span><span class="o" style="font-weight: 600;">=</span><span class="sc" style="color: #d14;">'_'</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
192
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC192" class="line" lang="java"> <span class="n" style="color: #333;">initial</span><span class="o" style="font-weight: 600;">=</span><span class="nc" style="color: #458; font-weight: 600;">Tools</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">indexOf</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">,</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="o" style="font-weight: 600;">)</span><span class="n" style="color: #333;">delimiter</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
193
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC193" 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;">initial</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 class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
194
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC194" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
195
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<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="nc" style="color: #458; font-weight: 600;">Tools</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isDigit</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">initial</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">])){</span><span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;}</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
196
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC196" class="line" lang="java"> </span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
197
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC197" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">number</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="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
198
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC198" 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;">initial</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;">s</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>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
199
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC199" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">byte</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">];</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
200
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC200" 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;">c</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">delimiter</span><span class="o" style="font-weight: 600;">){</span><span class="k" style="font-weight: 600;">break</span><span class="o" style="font-weight: 600;">;}</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
201
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC201" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Tools</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isDigit</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">));</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
202
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC202" class="line" lang="java"> <span class="n" style="color: #333;">number</span><span class="o" style="font-weight: 600;">=(</span><span class="n" style="color: #333;">number</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;">c</span><span class="o" style="font-weight: 600;">-</span><span class="sc" style="color: #d14;">'0'</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
203
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC203" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
204
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC204" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</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;">number</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
205
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC205" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
206
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC206" class="line" lang="java"> </span>
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<td class="new_line diff-line-num new" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
207
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC207" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/** Parse a gi number, or return -1 if formatted incorrectly. */</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
208
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC208" class="line" lang="java"> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">parseNcbiNumber</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">delimiter</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
209
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC209" 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;">s</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;">s</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="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;}</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
210
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<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="nc" style="color: #458; font-weight: 600;">Tools</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="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"ncbi"</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="nc" style="color: #458; font-weight: 600;">Tools</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="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">">ncbi"</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="nc" style="color: #458; font-weight: 600;">Tools</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="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"tid"</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="nc" style="color: #458; font-weight: 600;">Tools</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="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">">tid"</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 class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;}</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
211
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC211" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">initial</span><span class="o" style="font-weight: 600;">=</span><span class="nc" style="color: #458; font-weight: 600;">Tools</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">indexOf</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">,</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="o" style="font-weight: 600;">)</span><span class="n" style="color: #333;">delimiter</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
212
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC212" 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;">initial</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="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
213
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC213" class="line" lang="java"> <span class="n" style="color: #333;">delimiter</span><span class="o" style="font-weight: 600;">=</span><span class="sc" style="color: #d14;">'_'</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
214
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC214" class="line" lang="java"> <span class="n" style="color: #333;">initial</span><span class="o" style="font-weight: 600;">=</span><span class="nc" style="color: #458; font-weight: 600;">Tools</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">indexOf</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">,</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="o" style="font-weight: 600;">)</span><span class="n" style="color: #333;">delimiter</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
215
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC215" 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;">initial</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 class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;}</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
216
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC216" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
217
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<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="nc" style="color: #458; font-weight: 600;">Tools</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isDigit</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">initial</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">])){</span><span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
218
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC218" class="line" lang="java"> </span>
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<td class="new_line diff-line-num new" data-linenumber="219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
219
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC219" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">number</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="new_line diff-line-num new" data-linenumber="220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
220
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC220" 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;">initial</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;">s</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>
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<td class="new_line diff-line-num new" data-linenumber="221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
221
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC221" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">byte</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">];</span></span>
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<td class="new_line diff-line-num new" data-linenumber="222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
222
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC222" 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;">c</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">delimiter</span><span class="o" style="font-weight: 600;">){</span><span class="k" style="font-weight: 600;">break</span><span class="o" style="font-weight: 600;">;}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
223
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC223" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Tools</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isDigit</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">));</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
224
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC224" class="line" lang="java"> <span class="n" style="color: #333;">number</span><span class="o" style="font-weight: 600;">=(</span><span class="n" style="color: #333;">number</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;">c</span><span class="o" style="font-weight: 600;">-</span><span class="sc" style="color: #d14;">'0'</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
225
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC225" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
226
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC226" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">number</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
227
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC227" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
228
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC228" class="line" lang="java"></span>
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<td class="new_line diff-line-num new" data-linenumber="229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
229
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC229" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">getID</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">){</span><span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">getID</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">,</span> <span class="sc" style="color: #d14;">'|'</span><span class="o" style="font-weight: 600;">);}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
230
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC230" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/** Get the taxID from a header starting with a taxID or gi number */</span></span>
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<td class="new_line diff-line-num new" data-linenumber="231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
231
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC231" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">getID</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">delimiter</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
232
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC232" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">parseGiNumber</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">delimiter</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
233
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC233" 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;">x</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="n" style="color: #333;">array</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">];}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
234
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC234" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="nf" style="color: #900; font-weight: 600;">parseNcbiNumber</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">delimiter</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="235" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
235
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC235" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
236
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC236" class="line" lang="java"> </span>
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<td class="new_line diff-line-num new" data-linenumber="237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
237
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC237" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/** Get the taxID from a gi number */</span></span>
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<td class="new_line diff-line-num new" data-linenumber="238" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
238
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC238" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">getID</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">gi</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
239
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC239" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">gi</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;">gi</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
240
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC240" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">gi</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;">MAX_VALUE</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">gi</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="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">MAX_VALUE</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
241
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC241" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">gi</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">array</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;">gi</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;">array</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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<td class="new_line diff-line-num new" data-linenumber="242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
242
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC242" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">array</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;">gi</span><span class="o" style="font-weight: 600;">];</span></span>
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<td class="new_line diff-line-num new" data-linenumber="243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
243
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC243" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
244
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC244" class="line" lang="java"> </span>
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<td class="new_line diff-line-num new" data-linenumber="245" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
245
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC245" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">initialize</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;">fname</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
246
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC246" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fname</span><span class="o" style="font-weight: 600;">!=</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
247
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC247" 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;">fileString</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;">fileString</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fname</span><span class="o" style="font-weight: 600;">)){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
248
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC248" class="line" lang="java"> <span class="kd" style="font-weight: 600;">synchronized</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">GiToTaxid</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">class</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
249
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC249" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">initialized</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">fileString</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;">fileString</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fname</span><span class="o" style="font-weight: 600;">)){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
250
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC250" class="line" lang="java"> <span class="n" style="color: #333;">fileString</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">fname</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
251
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC251" 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;">fname</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;">".int1d"</span><span class="o" style="font-weight: 600;">)){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
252
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC252" class="line" lang="java"> <span class="n" style="color: #333;">array</span><span class="o" style="font-weight: 600;">=</span><span class="nc" style="color: #458; font-weight: 600;">ReadWrite</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">read</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="na" style="color: #008080;">class</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">fname</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
253
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC253" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span><span class="k" style="font-weight: 600;">else</span><span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
254
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC254" class="line" lang="java"> <span class="n" style="color: #333;">array</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">makeArray</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fname</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="255" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
255
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC255" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
256
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC256" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
257
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC257" class="line" lang="java"> <span class="n" style="color: #333;">initialized</span><span class="o" style="font-weight: 600;">=</span><span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
258
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC258" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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259
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC259" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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260
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC260" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
261
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC261" class="line" lang="java"> </span>
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<td class="new_line diff-line-num new" data-linenumber="262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
262
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC262" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">isInitialized</span><span class="o" style="font-weight: 600;">(){</span><span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">initialized</span><span class="o" style="font-weight: 600;">;}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
263
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC263" class="line" lang="java"> </span>
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<td class="new_line diff-line-num new" data-linenumber="264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
264
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC264" 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;">synchronized</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">unload</span><span class="o" style="font-weight: 600;">(){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
265
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC265" class="line" lang="java"> <span class="n" style="color: #333;">array</span><span class="o" style="font-weight: 600;">=</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
266
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC266" class="line" lang="java"> <span class="n" style="color: #333;">fileString</span><span class="o" style="font-weight: 600;">=</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
267
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC267" class="line" lang="java"> <span class="n" style="color: #333;">initialized</span><span class="o" style="font-weight: 600;">=</span><span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
268
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC268" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
269
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC269" class="line" lang="java"> </span>
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<td class="new_line diff-line-num new" data-linenumber="270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
270
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC270" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="nf" style="color: #900; font-weight: 600;">makeArray</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;">fnames</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
271
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC271" 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;">split</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
272
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC272" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="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;">fnames</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;">split</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="n" style="color: #333;">fnames</span><span class="o" style="font-weight: 600;">};}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
273
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC273" 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;">fnames</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">indexOf</span><span class="o" style="font-weight: 600;">(</span><span class="sc" style="color: #d14;">','</span><span class="o" style="font-weight: 600;">)>=</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">){</span><span class="n" style="color: #333;">split</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">fnames</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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<td class="new_line diff-line-num new" data-linenumber="274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
274
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC274" 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;">fnames</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">indexOf</span><span class="o" style="font-weight: 600;">(</span><span class="sc" style="color: #d14;">'#'</span><span class="o" style="font-weight: 600;">)>=</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
275
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC275" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fnames</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">indexOf</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="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"Note: Wildcard # only works for relative paths in present working directory."</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
276
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC276" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">File</span> <span class="n" style="color: #333;">dir</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;">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;">"user.dir"</span><span class="o" style="font-weight: 600;">));</span></span>
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<td class="new_line diff-line-num new" data-linenumber="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
277
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC277" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">prefix</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">fnames</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">substring</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;">fnames</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">indexOf</span><span class="o" style="font-weight: 600;">(</span><span class="sc" style="color: #d14;">'#'</span><span class="o" style="font-weight: 600;">));</span></span>
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<td class="new_line diff-line-num new" data-linenumber="278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
278
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC278" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">suffix</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">fnames</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">substring</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fnames</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">indexOf</span><span class="o" style="font-weight: 600;">(</span><span class="sc" style="color: #d14;">'#'</span><span class="o" style="font-weight: 600;">)+</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
279
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC279" class="line" lang="java"> </span>
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<td class="new_line diff-line-num new" data-linenumber="280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
280
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC280" 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;">array</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">dir</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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<td class="new_line diff-line-num new" data-linenumber="281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
281
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC281" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">StringBuilder</span> <span class="n" style="color: #333;">sb</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;">StringBuilder</span><span class="o" style="font-weight: 600;">();</span></span>
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<td class="new_line diff-line-num new" data-linenumber="282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
282
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC282" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">comma</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">""</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
283
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC283" 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;">File</span> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">array</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
284
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC284" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">s</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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<td class="new_line diff-line-num new" data-linenumber="285" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
285
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC285" 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;">s</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="n" style="color: #333;">prefix</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">startsWith</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">suffix</span><span class="o" style="font-weight: 600;">)){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="286" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
286
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC286" 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;">comma</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="287" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
287
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC287" 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;">s</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="288" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
288
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC288" class="line" lang="java"> <span class="n" style="color: #333;">comma</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">","</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
289
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC289" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
290
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC290" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
291
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC291" class="line" lang="java"> <span class="n" style="color: #333;">split</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sb</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 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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<td class="new_line diff-line-num new" data-linenumber="292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
292
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC292" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span><span class="k" style="font-weight: 600;">else</span><span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
293
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC293" 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;">RuntimeException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Invalid file: "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">fnames</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="294" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
294
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC294" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
295
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC295" class="line" lang="java"> </span>
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<td class="new_line diff-line-num new" data-linenumber="296" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
296
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC296" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">IntList</span> <span class="n" style="color: #333;">list</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;">IntList</span><span class="o" style="font-weight: 600;">();</span></span>
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<td class="new_line diff-line-num new" data-linenumber="297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
297
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC297" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// assert(max<Integer.MAX_VALUE) : "Overflow.";</span></span>
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<td class="new_line diff-line-num new" data-linenumber="298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
298
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC298" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// int[] x=new int[(int)max+1];</span></span>
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<td class="new_line diff-line-num new" data-linenumber="299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
299
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC299" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// Arrays.fill(x, -1);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
300
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC300" class="line" lang="java"> </span>
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<td class="new_line diff-line-num new" data-linenumber="301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
301
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC301" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">long</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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<td class="new_line diff-line-num new" data-linenumber="302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
302
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC302" 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;">s</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">split</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
303
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC303" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">count</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">addToList</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">list</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
304
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC304" 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;">count</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
305
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC305" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
306
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC306" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">list</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">shrink</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">array</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
307
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC307" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
308
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC308" class="line" lang="java"> </span>
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<td class="new_line diff-line-num new" data-linenumber="309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
309
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC309" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="nf" style="color: #900; font-weight: 600;">addToList</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;">fname</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">IntList</span> <span class="n" style="color: #333;">list</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
310
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC310" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">warned</span><span class="o" style="font-weight: 600;">=</span><span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
311
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC311" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">ByteFile</span> <span class="n" style="color: #333;">bf</span><span class="o" style="font-weight: 600;">=</span><span class="nc" style="color: #458; font-weight: 600;">ByteFile</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">makeByteFile</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fname</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
312
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC312" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">long</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="n" style="color: #333;">invalid</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="new_line diff-line-num new" data-linenumber="313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
313
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC313" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">bf</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextLine</span><span class="o" style="font-weight: 600;">();</span></span>
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<td class="new_line diff-line-num new" data-linenumber="314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
314
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC314" 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;">line</span><span class="o" style="font-weight: 600;">!=</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
315
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC315" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="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="nc" style="color: #458; font-weight: 600;">Tools</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isDigit</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">line</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="c1" style="color: #998; font-style: italic;">//Invalid lines will end with tab or na</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
316
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC316" 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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<td class="new_line diff-line-num new" data-linenumber="317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
317
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC317" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tab2</span><span class="o" style="font-weight: 600;">=</span><span class="nc" style="color: #458; font-weight: 600;">Tools</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">indexOfNth</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">,</span> <span class="sc" style="color: #d14;">'\t'</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
318
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC318" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tab3</span><span class="o" style="font-weight: 600;">=</span><span class="nc" style="color: #458; font-weight: 600;">Tools</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">indexOfNth</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">,</span> <span class="sc" style="color: #d14;">'\t'</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;">tab2</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
319
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC319" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">tab2</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;">tab2</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">tab3</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">tab3</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #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;">tab2</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;">tab3</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;">line</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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<td class="new_line diff-line-num new" data-linenumber="320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
320
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC320" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">tab2</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">tab2</span><span class="o" style="font-weight: 600;">]==</span><span class="sc" style="color: #d14;">'\t'</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">tab2</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;">tab3</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">", '"</span><span class="o" style="font-weight: 600;">+</span><span class="k" style="font-weight: 600;">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;">line</span><span class="o" style="font-weight: 600;">)+</span><span class="s" style="color: #d14;">"'"</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
321
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC321" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">tab3</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">tab3</span><span class="o" style="font-weight: 600;">]==</span><span class="sc" style="color: #d14;">'\t'</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">tab2</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;">tab3</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">", '"</span><span class="o" style="font-weight: 600;">+</span><span class="k" style="font-weight: 600;">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;">line</span><span class="o" style="font-weight: 600;">)+</span><span class="s" style="color: #d14;">"'"</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
322
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC322" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// assert(false) : tab2+", "+tab3+", '"+new String(line)+"'";</span></span>
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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
323
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC323" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tid</span><span class="o" style="font-weight: 600;">=</span><span class="nc" style="color: #458; font-weight: 600;">Parse</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;">line</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">tab2</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;">tab3</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
324
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC324" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">gi</span><span class="o" style="font-weight: 600;">=</span><span class="nc" style="color: #458; font-weight: 600;">Parse</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;">line</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">tab3</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;">line</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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<td class="new_line diff-line-num new" 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: inherit;" align="right" bgcolor="#ddfbe6">
325
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC325" 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;">gi</span><span class="o" style="font-weight: 600;">>=</span><span class="nc" style="color: #458; font-weight: 600;">Shared</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">MAX_ARRAY_LEN</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">gi</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="c1" style="color: #998; font-style: italic;">//A gi over 2.5b was observed May 3, 2021.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
326
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC326" class="line" lang="java"> <span class="n" style="color: #333;">invalid</span><span class="o" style="font-weight: 600;">++;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
327
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC327" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span><span class="k" style="font-weight: 600;">else</span><span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
328
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC328" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">gi</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="s" style="color: #d14;">"tid="</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">tid</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">", gi="</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">gi</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">", line=\n'"</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;">line</span><span class="o" style="font-weight: 600;">)+</span><span class="s" style="color: #d14;">"'"</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
329
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC329" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">old</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">list</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;">gi</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
330
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC330" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">old</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;">old</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">tid</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"Contradictory entries for gi "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">gi</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;">old</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;">tid</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"\n'"</span><span class="o" style="font-weight: 600;">+</span><span class="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;">line</span><span class="o" style="font-weight: 600;">)+</span><span class="s" style="color: #d14;">"'\ntab2="</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">tab2</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">", tab3="</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">tab3</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="331" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
331
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC331" class="line" lang="java"> </span>
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<td class="new_line diff-line-num new" data-linenumber="332" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
332
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC332" class="line" lang="java"> <span class="n" style="color: #333;">list</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">set</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">gi</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">tid</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="333" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
333
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC333" class="line" lang="java"> </span>
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<td class="new_line diff-line-num new" data-linenumber="334" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
334
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC334" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//assert(x[gi]==-1 || x[gi]==ncbi) : "Contradictory entries for gi "+gi+": "+x[gi]+" -> "+ncbi;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="335" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
335
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC335" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// if(x[gi]!=-1 && x[gi]!=ncbi){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="336" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
336
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC336" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// if(!warned){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="337" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
337
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC337" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// System.err.println("***WARNING*** For file "+fname+":\n"+</span></span>
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<td class="new_line diff-line-num new" data-linenumber="338" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
338
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC338" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// ("Contradictory entries for gi "+gi+": mapped to both taxID "+x[gi]+" and taxID "+ncbi)+</span></span>
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<td class="new_line diff-line-num new" data-linenumber="339" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
339
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC339" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// "\nThis may be an error from NCBI and you may wish to report it, but it is\n"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="340" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
340
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC340" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// + "being suppressed because NCBI data is known to contain multi-mapped gi numbers,\n"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="341" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
341
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC341" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// + "at least between nucleotide and protein, and gi numbers are deprecated anyway.");</span></span>
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<td class="new_line diff-line-num new" data-linenumber="342" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
342
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC342" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// warned=true;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="343" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
343
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC343" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// }</span></span>
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<td class="new_line diff-line-num new" data-linenumber="344" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
344
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC344" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// }else{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="345" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
345
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC345" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// x[gi]=ncbi;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="346" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
346
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC346" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// }</span></span>
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<td class="new_line diff-line-num new" data-linenumber="347" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
347
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC347" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="348" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
348
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC348" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span><span class="k" style="font-weight: 600;">else</span><span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
349
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC349" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="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="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="n" style="color: #333;">fname</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;">count</span><span class="o" style="font-weight: 600;">);}</span><span class="c1" style="color: #998; font-style: italic;">//debug</span></span>
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<td class="new_line diff-line-num new" data-linenumber="350" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
350
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC350" class="line" lang="java"> <span class="n" style="color: #333;">invalid</span><span class="o" style="font-weight: 600;">++;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="351" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
351
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC351" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="352" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
352
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC352" class="line" lang="java"> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">bf</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextLine</span><span class="o" style="font-weight: 600;">();</span></span>
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<td class="new_line diff-line-num new" data-linenumber="353" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
353
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC353" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="354" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
354
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC354" 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;">verbose</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;">"Count: "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">count</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"; \tInvalid: "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">invalid</span><span class="o" style="font-weight: 600;">);}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="355" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
355
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC355" class="line" lang="java"> <span class="n" style="color: #333;">bf</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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<td class="new_line diff-line-num new" data-linenumber="356" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
356
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC356" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">count</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="357" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
357
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC357" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="358" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
358
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC358" class="line" lang="java"> </span>
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<td class="new_line diff-line-num new" data-linenumber="359" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
359
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC359" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// private static int[] makeArrayOld(String fnames){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="360" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
360
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC360" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// String[] split;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="361" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
361
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC361" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// if(new File(fnames).exists()){split=new String[] {fnames};}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="362" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
362
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC362" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// else{split=fnames.split(",");}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="363" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
363
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC363" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// </span></span>
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<td class="new_line diff-line-num new" data-linenumber="364" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
364
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC364" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// long max=0;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="365" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
365
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC365" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// for(String s : split){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="366" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
366
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC366" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// max=Tools.max(max, findMaxID(s));</span></span>
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<td class="new_line diff-line-num new" data-linenumber="367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
367
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC367" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// }</span></span>
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<td class="new_line diff-line-num new" data-linenumber="368" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
368
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC368" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// </span></span>
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<td class="new_line diff-line-num new" data-linenumber="369" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
369
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC369" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// assert(max<Integer.MAX_VALUE) : "Overflow.";</span></span>
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<td class="new_line diff-line-num new" data-linenumber="370" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
370
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC370" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// int[] x=new int[(int)max+1];</span></span>
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371
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC371" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// Arrays.fill(x, -1);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="372" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
372
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC372" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// </span></span>
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<td class="new_line diff-line-num new" data-linenumber="373" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
373
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC373" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// long total=0;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="374" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
374
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC374" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// for(String s : split){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="375" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
375
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC375" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// long count=fillArray(s, x);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="376" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
376
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC376" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// total+=count;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
377
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC377" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// }</span></span>
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<td class="new_line diff-line-num new" data-linenumber="378" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
378
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC378" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// return x;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="379" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
379
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC379" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// }</span></span>
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<td class="new_line diff-line-num new" data-linenumber="380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
380
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC380" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// </span></span>
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<td class="new_line diff-line-num new" data-linenumber="381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
381
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC381" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// private static long findMaxID(String fname){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="382" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
382
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC382" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// ByteFile bf=ByteFile.makeByteFile(fname, true);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
383
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC383" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// long count=0, max=0;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
384
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC384" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// byte[] line=bf.nextLine();</span></span>
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<td class="new_line diff-line-num new" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
385
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC385" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// while(line!=null){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
386
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC386" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// count++;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="387" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
387
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC387" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// int tab=Tools.indexOf(line, (byte)'\t');</span></span>
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<td class="new_line diff-line-num new" data-linenumber="388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
388
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC388" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// long gi=Parse.parseLong(line, 0, tab);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
389
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC389" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// max=Tools.max(max, gi);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
390
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC390" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// line=bf.nextLine();</span></span>
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<td class="new_line diff-line-num new" data-linenumber="391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
391
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC391" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// }</span></span>
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<td class="new_line diff-line-num new" data-linenumber="392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
392
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC392" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// bf.close();</span></span>
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<td class="new_line diff-line-num new" data-linenumber="393" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
393
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC393" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// return max;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
394
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC394" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// }</span></span>
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<td class="new_line diff-line-num new" data-linenumber="395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
395
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC395" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// </span></span>
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<td class="new_line diff-line-num new" data-linenumber="396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
396
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC396" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// private static long fillArray(String fname, int[] x){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
397
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC397" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// boolean warned=false;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
398
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC398" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// ByteFile bf=ByteFile.makeByteFile(fname, true);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
399
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC399" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// long count=0;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="400" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
400
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC400" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// byte[] line=bf.nextLine();</span></span>
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<td class="new_line diff-line-num new" data-linenumber="401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
401
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC401" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// while(line!=null){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
402
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC402" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// count++;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
403
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC403" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// int tab=Tools.indexOf(line, (byte)'\t');</span></span>
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<td class="new_line diff-line-num new" data-linenumber="404" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
404
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC404" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// int gi=Parse.parseInt(line, 0, tab);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
405
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC405" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// int ncbi=Parse.parseInt(line, tab+1, line.length);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
406
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC406" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// //assert(x[gi]==-1 || x[gi]==ncbi) : "Contradictory entries for gi "+gi+": "+x[gi]+" -> "+ncbi;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="407" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
407
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC407" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// if(x[gi]!=-1 && x[gi]!=ncbi){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="408" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
408
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC408" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// if(!warned){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
409
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC409" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// System.err.println("***WARNING*** For file "+fname+":\n"+</span></span>
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<td class="new_line diff-line-num new" data-linenumber="410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
410
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC410" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// ("Contradictory entries for gi "+gi+": mapped to both taxID "+x[gi]+" and taxID "+ncbi)+</span></span>
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<td class="new_line diff-line-num new" data-linenumber="411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
411
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC411" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// "\nThis may be an error from NCBI and you may wish to report it, but it is\n"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
412
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC412" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// + "being suppressed because NCBI data is known to contain multi-mapped gi numbers,\n"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
413
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC413" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// + "at least between nucleotide and protein, and gi numbers are deprecated anyway.");</span></span>
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<td class="new_line diff-line-num new" data-linenumber="414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
414
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC414" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// warned=true;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
415
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC415" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// }</span></span>
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<td class="new_line diff-line-num new" data-linenumber="416" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
416
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC416" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// }else{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
417
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC417" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// x[gi]=ncbi;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="418" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
418
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC418" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// }</span></span>
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<td class="new_line diff-line-num new" data-linenumber="419" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
419
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC419" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// line=bf.nextLine();</span></span>
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<td class="new_line diff-line-num new" data-linenumber="420" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
420
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC420" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// }</span></span>
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<td class="new_line diff-line-num new" data-linenumber="421" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
421
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC421" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// if(verbose){System.err.println("Count: "+count);}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="422" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
422
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC422" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// bf.close();</span></span>
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<td class="new_line diff-line-num new" data-linenumber="423" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
423
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC423" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// return count;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="424" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
424
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC424" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// }</span></span>
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<td class="new_line diff-line-num new" data-linenumber="425" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
425
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC425" class="line" lang="java"> </span>
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<td class="new_line diff-line-num new" data-linenumber="426" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
426
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC426" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">array</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
427
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC427" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">fileString</span><span class="o" style="font-weight: 600;">;</span></span>
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428
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC428" class="line" lang="java"> </span>
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<td class="new_line diff-line-num new" data-linenumber="429" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
429
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC429" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">verbose</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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430
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC430" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">initialized</span><span class="o" style="font-weight: 600;">=</span><span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC431" class="line" lang="java"><span class="o" style="font-weight: 600;">}</span></span></pre></td>
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<a href="https://salsa.debian.org/med-team/bbmap/-/commit/1c662261847da712e5b04b94277f8aa712c37619#ef479b2702704ccabfeb99dfbba06448b794752b" style="color: #1068bf; text-decoration: none;"><strong style="font-weight: bold;">current/tax/TaxServer.java</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -1243,7 +1243,7 @@ public class TaxServer {</td>
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1243
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<td class="new_line diff-line-num" data-linenumber="1243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1243
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1243" 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;">type2</span><span class="o" style="font-weight: 600;">==</span><span class="no" style="color: #008080;">GI</span><span class="o" style="font-weight: 600;">){</span></span>
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1244
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<td class="new_line diff-line-num" data-linenumber="1244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1244
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1244" 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;">name</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">names</span><span class="o" style="font-weight: 600;">){</span></span>
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1245
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<td class="new_line diff-line-num" data-linenumber="1245" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1245
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1245" 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;">comma</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1246
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<td class="new_line diff-line-num old" data-linenumber="1246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC1246" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">TaxNode</span> <span class="n" style="color: #333;">tn</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">getTaxNodeGi</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff left deletion" style="background-color: #fac5cd;">Integer</span></span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parse<span class="idiff right deletion" style="background-color: #fac5cd;">Int</span></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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<td class="new_line diff-line-num new" data-linenumber="1246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1246
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1246" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">TaxNode</span> <span class="n" style="color: #333;">tn</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">getTaxNodeGi</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">Long</span></span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parse<span class="idiff right addition" style="background-color: #c7f0d2;">Long</span></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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1247
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<td class="new_line diff-line-num" data-linenumber="1247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1247
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1247" 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;">tn</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;">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;">"-1"</span><span class="o" style="font-weight: 600;">);}</span></span>
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1248
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<td class="new_line diff-line-num" data-linenumber="1248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1248
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1248" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span><span class="o" style="font-weight: 600;">{</span><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;">tn</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">id</span><span class="o" style="font-weight: 600;">);}</span></span>
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<td class="old_line diff-line-num" data-linenumber="1249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1249
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<td class="new_line diff-line-num" data-linenumber="1249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1249
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1249" class="line" lang="java"> <span class="n" style="color: #333;">comma</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">","</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -1297,7 +1297,7 @@ public class TaxServer {</td>
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<td class="old_line diff-line-num" data-linenumber="1297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1297
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<td class="new_line diff-line-num" data-linenumber="1297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1297
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1297" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">type2</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">type</span><span class="o" style="font-weight: 600;">&</span><span class="mi" style="color: #099;">15</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="1298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1298
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<td class="new_line diff-line-num" data-linenumber="1298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1298
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1298" class="line" lang="java"> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">TaxNode</span> <span class="n" style="color: #333;">tn</span><span class="o" style="font-weight: 600;">;</span></span>
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1299
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1299
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1299" 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;">type2</span><span class="o" style="font-weight: 600;">==</span><span class="no" style="color: #008080;">GI</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1300
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<td class="new_line diff-line-num old" data-linenumber="1300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC1300" class="line" lang="java"> <span class="n" style="color: #333;">tn</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">getTaxNodeGi</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff left deletion" style="background-color: #fac5cd;">Integer</span></span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parse<span class="idiff right deletion" style="background-color: #fac5cd;">Int</span></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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<td class="old_line diff-line-num new" data-linenumber="1301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1300
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1300" class="line" lang="java"> <span class="n" style="color: #333;">tn</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">getTaxNodeGi</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">Long</span></span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parse<span class="idiff right addition" style="background-color: #c7f0d2;">Long</span></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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<td class="old_line diff-line-num" data-linenumber="1301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1301
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<td class="new_line diff-line-num" data-linenumber="1301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1301
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1301" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span><span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">type2</span><span class="o" style="font-weight: 600;">==</span><span class="no" style="color: #008080;">NAME</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="old_line diff-line-num" data-linenumber="1302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1302
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<td class="new_line diff-line-num" data-linenumber="1302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1302
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1302" class="line" lang="java"> <span class="n" style="color: #333;">tn</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">getTaxNodeByName</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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<td class="old_line diff-line-num" data-linenumber="1303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1303
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<td class="new_line diff-line-num" data-linenumber="1303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1303
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1303" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span><span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">type2</span><span class="o" style="font-weight: 600;">==</span><span class="no" style="color: #008080;">TAXID</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="1348" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1348" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -1348,7 +1348,7 @@ public class TaxServer {</td>
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<td class="old_line diff-line-num" data-linenumber="1348" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1348
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<td class="new_line diff-line-num" data-linenumber="1348" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1348
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1348" 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;">type2</span><span class="o" style="font-weight: 600;">==</span><span class="no" style="color: #008080;">GI</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="old_line diff-line-num" data-linenumber="1349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1349
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<td class="new_line diff-line-num" data-linenumber="1349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1349
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1349" 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;">name</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">names</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="old_line diff-line-num" data-linenumber="1350" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1350
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<td class="new_line diff-line-num" data-linenumber="1350" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1350
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1350" 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;">comma</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1351" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1351
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<td class="new_line diff-line-num old" data-linenumber="1351" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC1351" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">TaxNode</span> <span class="n" style="color: #333;">tn</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">getTaxNodeGi</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff left deletion" style="background-color: #fac5cd;">Integer</span></span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parse<span class="idiff right deletion" style="background-color: #fac5cd;">Int</span></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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<td class="old_line diff-line-num new" data-linenumber="1352" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1351" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1351
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1351" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">TaxNode</span> <span class="n" style="color: #333;">tn</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">getTaxNodeGi</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">Long</span></span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parse<span class="idiff right addition" style="background-color: #c7f0d2;">Long</span></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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<td class="old_line diff-line-num" data-linenumber="1352" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1352
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<td class="new_line diff-line-num" data-linenumber="1352" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1352
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1352" 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;">tn</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;">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;">"Not found"</span><span class="o" style="font-weight: 600;">);}</span></span>
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<td class="old_line diff-line-num" data-linenumber="1353" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1353
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<td class="new_line diff-line-num" data-linenumber="1353" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1353
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1353" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span><span class="o" style="font-weight: 600;">{</span><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;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">toSemicolon</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">tn</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">skipNonCanonical</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">mononomial</span><span class="o" style="font-weight: 600;">));}</span></span>
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<td class="old_line diff-line-num" data-linenumber="1354" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1354
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<td class="new_line diff-line-num" data-linenumber="1354" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1354
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1354" class="line" lang="java"> <span class="n" style="color: #333;">comma</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">","</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -1414,7 +1414,7 @@ public class TaxServer {</td>
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1414
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1414
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1414" class="line" lang="java"> </span>
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<td class="old_line diff-line-num" data-linenumber="1415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1415
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<td class="new_line diff-line-num" data-linenumber="1415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1415
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1415" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">img</span><span class="o" style="font-weight: 600;">=-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="1416" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1416
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<td class="new_line diff-line-num" data-linenumber="1416" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1416
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1416" 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;">type</span><span class="o" style="font-weight: 600;">==</span><span class="no" style="color: #008080;">GI</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1417
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<td class="new_line diff-line-num old" data-linenumber="1417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC1417" class="line" lang="java"> <span class="n" style="color: #333;">tn0</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">getTaxNodeGi</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff left deletion" style="background-color: #fac5cd;">Integer</span></span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parse<span class="idiff right deletion" style="background-color: #fac5cd;">Int</span></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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<td class="old_line diff-line-num new" data-linenumber="1418" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1417
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1417" class="line" lang="java"> <span class="n" style="color: #333;">tn0</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">getTaxNodeGi</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">Long</span></span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parse<span class="idiff right addition" style="background-color: #c7f0d2;">Long</span></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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1418
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<td class="new_line diff-line-num" data-linenumber="1418" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1418
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1418" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span><span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">type</span><span class="o" style="font-weight: 600;">==</span><span class="no" style="color: #008080;">NAME</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="old_line diff-line-num" data-linenumber="1419" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1419
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<td class="new_line diff-line-num" data-linenumber="1419" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1419
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1419" class="line" lang="java"> <span class="n" style="color: #333;">tn0</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">getTaxNodeByName</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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1420
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1420
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1420" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span><span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">type</span><span class="o" style="font-weight: 600;">==</span><span class="no" style="color: #008080;">TAXID</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="1546" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1546" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -1546,7 +1546,7 @@ public class TaxServer {</td>
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<td class="old_line diff-line-num" data-linenumber="1546" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1546
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<td class="new_line diff-line-num" data-linenumber="1546" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1546
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1546" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">type2</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">type</span><span class="o" style="font-weight: 600;">&</span><span class="mi" style="color: #099;">15</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="1547" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1547
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<td class="new_line diff-line-num" data-linenumber="1547" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1547
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1547" 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;">type2</span><span class="o" style="font-weight: 600;">==</span><span class="no" style="color: #008080;">GI</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="old_line diff-line-num" data-linenumber="1548" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1548
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<td class="new_line diff-line-num" data-linenumber="1548" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1548
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1548" 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;">name</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">names</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1549" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1549
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<td class="new_line diff-line-num old" data-linenumber="1549" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC1549" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">TaxNode</span> <span class="n" style="color: #333;">tn</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">getTaxNodeGi</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff left deletion" style="background-color: #fac5cd;">Integer</span></span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parse<span class="idiff right deletion" style="background-color: #fac5cd;">Int</span></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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<td class="new_line diff-line-num new" data-linenumber="1549" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1549
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1549" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">TaxNode</span> <span class="n" style="color: #333;">tn</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">getTaxNodeGi</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">Long</span></span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parse<span class="idiff right addition" style="background-color: #c7f0d2;">Long</span></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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1550
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<td class="new_line diff-line-num" data-linenumber="1550" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1550
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1550" 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;">tn</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;">list</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;">tn</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">id</span><span class="o" style="font-weight: 600;">);}</span></span>
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1551
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1551
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1551" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span><span class="o" style="font-weight: 600;">{</span><span class="n" style="color: #333;">notFound</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">incrementAndGet</span><span class="o" style="font-weight: 600;">();}</span></span>
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1552
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1552" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1620" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1620" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -1620,7 +1620,7 @@ public class TaxServer {</td>
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1620
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1620
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1620" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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1621
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1621
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1621" class="line" lang="java"> </span>
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<td class="old_line diff-line-num" data-linenumber="1622" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1622
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<td class="new_line diff-line-num" data-linenumber="1622" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1622
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1622" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/** Look up a TaxNode from the gi number */</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1623" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1623
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<td class="new_line diff-line-num old" data-linenumber="1623" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC1623" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">TaxNode</span> <span class="nf" style="color: #900; font-weight: 600;">getTaxNodeGi</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right deletion" style="background-color: #fac5cd;">int</span></span> <span class="n" style="color: #333;">gi</span><span class="o" style="font-weight: 600;">){</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1624" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1623" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1623
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1623" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">TaxNode</span> <span class="nf" style="color: #900; font-weight: 600;">getTaxNodeGi</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right addition" style="background-color: #c7f0d2;">long</span></span> <span class="n" style="color: #333;">gi</span><span class="o" style="font-weight: 600;">){</span></span>
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1624
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<td class="new_line diff-line-num" data-linenumber="1624" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1624
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1624" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ncbi</span><span class="o" style="font-weight: 600;">=-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="1625" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1625
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<td class="new_line diff-line-num" data-linenumber="1625" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1625
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1625" 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="old_line diff-line-num" data-linenumber="1626" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1626
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<td class="new_line diff-line-num" data-linenumber="1626" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1626
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1626" class="line" lang="java"> <span class="n" style="color: #333;">ncbi</span><span class="o" style="font-weight: 600;">=</span><span class="nc" style="color: #458; font-weight: 600;">GiToTaxid</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="n" style="color: #333;">gi</span><span class="o" style="font-weight: 600;">);</span></span>
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<a href="https://salsa.debian.org/med-team/bbmap/-/commit/1c662261847da712e5b04b94277f8aa712c37619#f983ca3b863aeefdc8a5af4feffca4582a7fa91d" style="color: #1068bf; text-decoration: none;"><strong style="font-weight: bold;">current/tax/TaxTree.java</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2491" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2491" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -2491,7 +2491,8 @@ public class TaxTree implements Serializable{</td>
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2491
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2491
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2491" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">default18SFileIGBVM</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"/data/sketch/silva/18S_consensus_with_silva_maxns10_taxsorted.fa.gz"</span><span class="o" style="font-weight: 600;">;</span></span>
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2492
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2492
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2492" class="line" lang="java"> </span>
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2493
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<td class="new_line diff-line-num" data-linenumber="2493" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
2493
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2493" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">defaultImgFile</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"TAX_PATH/imgDump.txt"</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2494" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
2494
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<td class="new_line diff-line-num old" data-linenumber="2494" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC2494" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">defaultTableFile</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"TAX_PATH/gitable.int1d.gz"</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2494" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2494
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC2494" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">defaultTableFileInt</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"TAX_PATH/gitable.int1d.gz"</span><span class="o" style="font-weight: 600;">;</span></span>
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2495
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC2495" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">defaultTableFile</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"TAX_PATH/gitable.int2d.gz"</span><span class="o" style="font-weight: 600;">;</span></span>
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2495
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<td class="new_line diff-line-num" data-linenumber="2496" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
2496
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2496" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">defaultTreeFile</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"TAX_PATH/tree.taxtree.gz"</span><span class="o" style="font-weight: 600;">;</span></span>
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2496
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<td class="new_line diff-line-num" data-linenumber="2497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
2497
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2497" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">defaultPatternFile</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"TAX_PATH/patterns.txt"</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="2497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
2497
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<td class="new_line diff-line-num" data-linenumber="2498" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
2498
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2498" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">defaultSizeFile</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"TAX_PATH/taxsize.tsv.gz"</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="2526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -2526,7 +2527,7 @@ public class TaxTree implements Serializable{</td>
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<td class="old_line diff-line-num" data-linenumber="2526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
2526
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<td class="new_line diff-line-num" data-linenumber="2527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
2527
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2527" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/** Path to all taxonomy files, substituted in to make specific file paths */</span></span>
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<td class="old_line diff-line-num" data-linenumber="2527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
2527
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<td class="new_line diff-line-num" data-linenumber="2528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
2528
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2528" 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="no" style="color: #008080;">TAX_PATH</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">defaultTaxPath</span><span class="o" style="font-weight: 600;">();</span></span>
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<td class="old_line diff-line-num" data-linenumber="2528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
2528
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<td class="new_line diff-line-num" data-linenumber="2529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
2529
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2529" class="line" lang="java"> </span>
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<td class="old_line diff-line-num old" data-linenumber="2529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
2529
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<td class="new_line diff-line-num old" data-linenumber="2530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC2529" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/** Location of gitable.int<span class="idiff left right deletion" style="background-color: #fac5cd;">1</span>d.gz for gi lookups */</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2530
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC2530" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/** Location of gitable.int<span class="idiff left right addition" style="background-color: #c7f0d2;">2</span>d.gz for gi lookups */</span></span>
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2530
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<td class="new_line diff-line-num" data-linenumber="2531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
2531
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2531" 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="nf" style="color: #900; font-weight: 600;">defaultTableFile</span><span class="o" style="font-weight: 600;">(){</span><span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">defaultTableFile</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;">"TAX_PATH"</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">TAX_PATH</span><span class="o" style="font-weight: 600;">);}</span></span>
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2531
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<td class="new_line diff-line-num" data-linenumber="2532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
2532
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2532" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/** Location of tree.taxtree.gz */</span></span>
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2532
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<td class="new_line diff-line-num" data-linenumber="2533" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
2533
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2533" 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="nf" style="color: #900; font-weight: 600;">defaultTreeFile</span><span class="o" style="font-weight: 600;">(){</span><span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">defaultTreeFile</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;">"TAX_PATH"</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">TAX_PATH</span><span class="o" style="font-weight: 600;">);}</span></span>
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<a href="https://salsa.debian.org/med-team/bbmap/-/commit/1c662261847da712e5b04b94277f8aa712c37619#2f1f31317e182ac33d5588ced7cd3e1807d82495" style="color: #1068bf; text-decoration: none;"><strong style="font-weight: bold;">docs/changelog.txt</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="897" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="897" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -897,6 +897,10 @@ Wrapped instances of byte array instantiation in allocByte1D.</td>
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<td class="old_line diff-line-num" data-linenumber="897" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
897
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<td class="new_line diff-line-num" data-linenumber="897" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
897
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC897" class="line" lang="plaintext">38.91</span>
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898
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<td class="new_line diff-line-num" data-linenumber="898" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
898
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC898" class="line" lang="plaintext">Fixed SendSketch json array format for very large input, on client side.</span>
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<td class="old_line diff-line-num" data-linenumber="899" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
899
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<td class="new_line diff-line-num" data-linenumber="899" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
899
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC899" class="line" lang="plaintext">Added maxload flag to BBCMS.</span>
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900
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC900" class="line" lang="plaintext">38.97</span>
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<td class="new_line diff-line-num new" data-linenumber="901" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
901
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC901" class="line" lang="plaintext">Added trimtips to BBDuk, mainly for trimming adapters on both ends of PacBio reads.</span>
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<td class="new_line diff-line-num new" data-linenumber="902" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
902
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC902" class="line" lang="plaintext">Changed processing of reads longer than 200bp to force ASCII-33 quality.</span>
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<td class="new_line diff-line-num new" data-linenumber="903" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
903
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC903" class="line" lang="plaintext">Enable automatic entryfilter in Clumpify to handle libraries with mostly identical reads.</span>
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900
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<td class="new_line diff-line-num" data-linenumber="904" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
904
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC904" class="line" lang="plaintext"></span>
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901
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905
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC905" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num" data-linenumber="902" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
902
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<td class="new_line diff-line-num" data-linenumber="906" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
906
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC906" class="line" lang="plaintext">todo: outshort for fungalrelease.</span>
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<a href="https://salsa.debian.org/med-team/bbmap/-/commit/1c662261847da712e5b04b94277f8aa712c37619#9987ab0d56f16295f54349f6c81020fd130981e3" style="color: #1068bf; text-decoration: none;"><strong style="font-weight: bold;">removecatdogmousehuman.sh</strong></a>
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<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -3,7 +3,7 @@</td>
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<td class="old_line diff-line-num" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
3
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<td class="new_line diff-line-num" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
3
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC3" class="line" lang="shell">usage<span class="o" style="font-weight: 600;">(){</span></span>
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4
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<td class="new_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
4
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC4" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span></span>
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5
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<td class="new_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
5
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC5" class="line" lang="shell"><span class="s2" style="color: #d14;">Written by Brian Bushnell</span></span>
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<td class="old_line diff-line-num old" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
6
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<td class="new_line diff-line-num old" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC6" class="line" lang="shell"><span class="s2" style="color: #d14;">Last modified <span class="idiff left deletion" style="background-color: #fac5cd;">Sept</span>ember <span class="idiff deletion" style="background-color: #fac5cd;">17</span>, 201<span class="idiff right deletion" style="background-color: #fac5cd;">8</span></span></span>
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<td class="old_line diff-line-num new" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
6
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC6" class="line" lang="shell"><span class="s2" style="color: #d14;">Last modified <span class="idiff left addition" style="background-color: #c7f0d2;">Dec</span>ember <span class="idiff addition" style="background-color: #c7f0d2;">22</span>, 20<span class="idiff right addition" style="background-color: #c7f0d2;">2</span>1</span></span>
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7
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<td class="new_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
7
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC7" class="line" lang="shell"><span class="s2" style="color: #d14;">This script requires at least 52GB RAM.</span></span>
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<td class="old_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
8
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<td class="new_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
8
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC8" class="line" lang="shell"><span class="s2" style="color: #d14;">It is designed for NERSC and uses hard-coded paths.</span></span>
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9
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<td class="new_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
9
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC9" class="line" lang="shell"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -68,7 +68,7 @@ calcXmx () {</td>
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68
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<td class="new_line diff-line-num" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
68
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC68" class="line" lang="shell">calcXmx <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$@</span><span class="s2" style="color: #d14;">"</span></span>
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69
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<td class="new_line diff-line-num" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
69
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC69" class="line" lang="shell"></span>
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<td class="old_line diff-line-num" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
70
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<td class="new_line diff-line-num" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
70
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC70" class="line" lang="shell"><span class="k" style="font-weight: 600;">function </span>removecatdogmousehuman<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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<td class="new_line diff-line-num old" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC71" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">local </span><span class="nv" style="color: #008080;">CMD</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"java </span><span class="nv" style="color: #008080;">$EA</span><span class="s2" style="color: #d14;"> </span><span class="nv" style="color: #008080;">$EOOM</span><span class="s2" style="color: #d14;"> </span><span class="nv" style="color: #008080;">$z</span><span class="s2" style="color: #d14;"> </span><span class="nv" style="color: #008080;">$z2</span><span class="s2" style="color: #d14;"> </span><span class="nv" style="color: #008080;">$JNI</span><span class="s2" style="color: #d14;"> -cp </span><span class="nv" style="color: #008080;">$CP</span><span class="s2" style="color: #d14;"> align2.BBMap minratio=0.9 maxindel=3 bwr=0.16 bw=12 quickmatch fast minhits=2 path=/global/<span class="idiff left right deletion" style="background-color: #fac5cd;">projectb/sandbox/gaag</span>/bbtools/mousecatdoghuman/ pigz unpigz zl=6 qtrim=r trimq=10 untrim idtag usemodulo printunmappedcount ztd=2 kfilter=25 maxsites=1 k=14 bloomfilter </span><span class="nv" style="color: #008080;">$@</span><span class="s2" style="color: #d14;">"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
71
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC71" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">local </span><span class="nv" style="color: #008080;">CMD</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"java </span><span class="nv" style="color: #008080;">$EA</span><span class="s2" style="color: #d14;"> </span><span class="nv" style="color: #008080;">$EOOM</span><span class="s2" style="color: #d14;"> </span><span class="nv" style="color: #008080;">$z</span><span class="s2" style="color: #d14;"> </span><span class="nv" style="color: #008080;">$z2</span><span class="s2" style="color: #d14;"> </span><span class="nv" style="color: #008080;">$JNI</span><span class="s2" style="color: #d14;"> -cp </span><span class="nv" style="color: #008080;">$CP</span><span class="s2" style="color: #d14;"> align2.BBMap minratio=0.9 maxindel=3 bwr=0.16 bw=12 quickmatch fast minhits=2 path=/global/<span class="idiff left right addition" style="background-color: #c7f0d2;">cfs/cdirs</span>/bbtools/mousecatdoghuman/ pigz unpigz zl=6 qtrim=r trimq=10 untrim idtag usemodulo printunmappedcount ztd=2 kfilter=25 maxsites=1 k=14 bloomfilter </span><span class="nv" style="color: #008080;">$@</span><span class="s2" style="color: #d14;">"</span></span>
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72
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<td class="new_line diff-line-num" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
72
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC72" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$CMD</span> <span class="o" style="font-weight: 600;">></span>&2</span>
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<td class="old_line diff-line-num" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
73
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<td class="new_line diff-line-num" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
73
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC73" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">eval</span> <span class="nv" style="color: #008080;">$CMD</span></span>
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74
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<td class="new_line diff-line-num" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
74
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC74" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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<a href="https://salsa.debian.org/med-team/bbmap/-/commit/1c662261847da712e5b04b94277f8aa712c37619#20e87219ac67aaa797f562324d1b104fc07b648f" style="color: #1068bf; text-decoration: none;"><strong style="font-weight: bold;">removehuman.sh</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -3,7 +3,7 @@</td>
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<td class="old_line diff-line-num" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
3
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<td class="new_line diff-line-num" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
3
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC3" class="line" lang="shell">usage<span class="o" style="font-weight: 600;">(){</span></span>
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4
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<td class="new_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
4
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC4" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
5
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<td class="new_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
5
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC5" class="line" lang="shell"><span class="s2" style="color: #d14;">Written by Brian Bushnell</span></span>
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<td class="old_line diff-line-num old" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
6
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<td class="new_line diff-line-num old" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC6" class="line" lang="shell"><span class="s2" style="color: #d14;">Last modified <span class="idiff left deletion" style="background-color: #fac5cd;">Sept</span>ember <span class="idiff deletion" style="background-color: #fac5cd;">17</span>, 201<span class="idiff right deletion" style="background-color: #fac5cd;">8</span></span></span>
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<td class="old_line diff-line-num new" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
6
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC6" class="line" lang="shell"><span class="s2" style="color: #d14;">Last modified <span class="idiff left addition" style="background-color: #c7f0d2;">Dec</span>ember <span class="idiff addition" style="background-color: #c7f0d2;">22</span>, 20<span class="idiff right addition" style="background-color: #c7f0d2;">2</span>1</span></span>
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7
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<td class="new_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
7
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC7" class="line" lang="shell"><span class="s2" style="color: #d14;">This script requires at least 16GB RAM.</span></span>
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8
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<td class="new_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
8
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC8" class="line" lang="shell"><span class="s2" style="color: #d14;">It is designed for NERSC and uses hard-coded paths.</span></span>
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9
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<td class="new_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
9
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC9" class="line" lang="shell"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -66,7 +66,7 @@ calcXmx () {</td>
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66
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<td class="new_line diff-line-num" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
66
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC66" class="line" lang="shell">calcXmx <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$@</span><span class="s2" style="color: #d14;">"</span></span>
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67
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC67" class="line" lang="shell"></span>
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68
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC68" class="line" lang="shell"><span class="k" style="font-weight: 600;">function </span>removehuman<span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
69
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<td class="new_line diff-line-num old" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC69" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">local </span><span class="nv" style="color: #008080;">CMD</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"java </span><span class="nv" style="color: #008080;">$EA</span><span class="s2" style="color: #d14;"> </span><span class="nv" style="color: #008080;">$EOOM</span><span class="s2" style="color: #d14;"> </span><span class="nv" style="color: #008080;">$z</span><span class="s2" style="color: #d14;"> </span><span class="nv" style="color: #008080;">$z2</span><span class="s2" style="color: #d14;"> </span><span class="nv" style="color: #008080;">$JNI</span><span class="s2" style="color: #d14;"> -cp </span><span class="nv" style="color: #008080;">$CP</span><span class="s2" style="color: #d14;"> align2.BBMap minratio=0.9 maxindel=3 bwr=0.16 bw=12 quickmatch fast minhits=2 path=/global/<span class="idiff left right deletion" style="background-color: #fac5cd;">projectb/sandbox/gaag</span>/bbtools/hg19 pigz unpigz zl=6 qtrim=r trimq=10 untrim idtag usemodulo printunmappedcount ztd=2 kfilter=25 maxsites=1 k=14 bloomfilter </span><span class="nv" style="color: #008080;">$@</span><span class="s2" style="color: #d14;">"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
69
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC69" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">local </span><span class="nv" style="color: #008080;">CMD</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"java </span><span class="nv" style="color: #008080;">$EA</span><span class="s2" style="color: #d14;"> </span><span class="nv" style="color: #008080;">$EOOM</span><span class="s2" style="color: #d14;"> </span><span class="nv" style="color: #008080;">$z</span><span class="s2" style="color: #d14;"> </span><span class="nv" style="color: #008080;">$z2</span><span class="s2" style="color: #d14;"> </span><span class="nv" style="color: #008080;">$JNI</span><span class="s2" style="color: #d14;"> -cp </span><span class="nv" style="color: #008080;">$CP</span><span class="s2" style="color: #d14;"> align2.BBMap minratio=0.9 maxindel=3 bwr=0.16 bw=12 quickmatch fast minhits=2 path=/global/<span class="idiff left right addition" style="background-color: #c7f0d2;">cfs/cdirs</span>/bbtools/hg19 pigz unpigz zl=6 qtrim=r trimq=10 untrim idtag usemodulo printunmappedcount ztd=2 kfilter=25 maxsites=1 k=14 bloomfilter </span><span class="nv" style="color: #008080;">$@</span><span class="s2" style="color: #d14;">"</span></span>
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70
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<td class="new_line diff-line-num" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
70
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC70" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$CMD</span> <span class="o" style="font-weight: 600;">></span>&2</span>
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<td class="old_line diff-line-num" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
71
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<td class="new_line diff-line-num" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
71
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC71" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">eval</span> <span class="nv" style="color: #008080;">$CMD</span></span>
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<td class="old_line diff-line-num" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
72
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<td class="new_line diff-line-num" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
72
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC72" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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<a href="https://salsa.debian.org/med-team/bbmap/-/commit/1c662261847da712e5b04b94277f8aa712c37619#e3098a112479d051ffa11669086944ad085232cc" style="color: #1068bf; text-decoration: none;"><strong style="font-weight: bold;">removehuman2.sh</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -3,7 +3,7 @@</td>
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<td class="old_line diff-line-num" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
3
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<td class="new_line diff-line-num" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
3
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC3" class="line" lang="shell">usage<span class="o" style="font-weight: 600;">(){</span></span>
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4
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<td class="new_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
4
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC4" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
5
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<td class="new_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
5
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC5" class="line" lang="shell"><span class="s2" style="color: #d14;">Written by Brian Bushnell</span></span>
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<td class="old_line diff-line-num old" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
6
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<td class="new_line diff-line-num old" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC6" class="line" lang="shell"><span class="s2" style="color: #d14;">Last modified <span class="idiff left deletion" style="background-color: #fac5cd;">Sept</span>ember <span class="idiff deletion" style="background-color: #fac5cd;">17</span>, 201<span class="idiff right deletion" style="background-color: #fac5cd;">8</span></span></span>
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<td class="old_line diff-line-num new" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
6
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC6" class="line" lang="shell"><span class="s2" style="color: #d14;">Last modified <span class="idiff left addition" style="background-color: #c7f0d2;">Dec</span>ember <span class="idiff addition" style="background-color: #c7f0d2;">22</span>, 20<span class="idiff right addition" style="background-color: #c7f0d2;">2</span>1</span></span>
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<td class="old_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
7
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<td class="new_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
7
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC7" class="line" lang="shell"><span class="s2" style="color: #d14;">This script requires at least 17GB RAM.</span></span>
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<td class="old_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
8
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<td class="new_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
8
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC8" class="line" lang="shell"><span class="s2" style="color: #d14;">It is designed for NERSC and uses hard-coded paths.</span></span>
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9
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<td class="new_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
9
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC9" class="line" lang="shell"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -62,7 +62,7 @@ calcXmx () {</td>
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62
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<td class="new_line diff-line-num" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
62
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC62" class="line" lang="shell">calcXmx <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$@</span><span class="s2" style="color: #d14;">"</span></span>
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63
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63
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC63" class="line" lang="shell"></span>
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64
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<td class="new_line diff-line-num" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
64
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC64" class="line" lang="shell"><span class="k" style="font-weight: 600;">function </span>removehuman<span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
65
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<td class="new_line diff-line-num old" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC65" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">local </span><span class="nv" style="color: #008080;">CMD</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"java </span><span class="nv" style="color: #008080;">$EA</span><span class="s2" style="color: #d14;"> </span><span class="nv" style="color: #008080;">$EOOM</span><span class="s2" style="color: #d14;"> </span><span class="nv" style="color: #008080;">$z</span><span class="s2" style="color: #d14;"> </span><span class="nv" style="color: #008080;">$z2</span><span class="s2" style="color: #d14;"> </span><span class="nv" style="color: #008080;">$JNI</span><span class="s2" style="color: #d14;"> -cp </span><span class="nv" style="color: #008080;">$CP</span><span class="s2" style="color: #d14;"> align2.BBMap minratio=0.75 maxindel=8 bwr=0.22 bw=26 minhits=1 path=/global/<span class="idiff left right deletion" style="background-color: #fac5cd;">projectb/sandbox/gaag</span>/bbtools/hg19 build=2 pigz unpigz zl=6 qtrim=r trimq=10 untrim idtag usemodulo printunmappedcount ztd=2 maxsites=1 k=14 tipsearch=0 kfilter=25 bloomfilter </span><span class="nv" style="color: #008080;">$@</span><span class="s2" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num new" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
65
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC65" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">local </span><span class="nv" style="color: #008080;">CMD</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"java </span><span class="nv" style="color: #008080;">$EA</span><span class="s2" style="color: #d14;"> </span><span class="nv" style="color: #008080;">$EOOM</span><span class="s2" style="color: #d14;"> </span><span class="nv" style="color: #008080;">$z</span><span class="s2" style="color: #d14;"> </span><span class="nv" style="color: #008080;">$z2</span><span class="s2" style="color: #d14;"> </span><span class="nv" style="color: #008080;">$JNI</span><span class="s2" style="color: #d14;"> -cp </span><span class="nv" style="color: #008080;">$CP</span><span class="s2" style="color: #d14;"> align2.BBMap minratio=0.75 maxindel=8 bwr=0.22 bw=26 minhits=1 path=/global/<span class="idiff left right addition" style="background-color: #c7f0d2;">cfs/cdirs</span>/bbtools/hg19 build=2 pigz unpigz zl=6 qtrim=r trimq=10 untrim idtag usemodulo printunmappedcount ztd=2 maxsites=1 k=14 tipsearch=0 kfilter=25 bloomfilter </span><span class="nv" style="color: #008080;">$@</span><span class="s2" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
66
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<td class="new_line diff-line-num" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
66
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC66" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$CMD</span> <span class="o" style="font-weight: 600;">></span>&2</span>
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<td class="old_line diff-line-num" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
67
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<td class="new_line diff-line-num" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
67
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC67" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">eval</span> <span class="nv" style="color: #008080;">$CMD</span></span>
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68
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<td class="new_line diff-line-num" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
68
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC68" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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<a href="https://salsa.debian.org/med-team/bbmap/-/commit/1c662261847da712e5b04b94277f8aa712c37619#098de73a43baa620dfd2d5bb4286132e821889eb" style="color: #1068bf; text-decoration: none;"><strong style="font-weight: bold;">removemicrobes.sh</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -3,7 +3,7 @@</td>
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<td class="old_line diff-line-num" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
3
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<td class="new_line diff-line-num" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
3
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC3" class="line" lang="shell">usage<span class="o" style="font-weight: 600;">(){</span></span>
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4
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<td class="new_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
4
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC4" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
5
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<td class="new_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
5
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC5" class="line" lang="shell"><span class="s2" style="color: #d14;">Written by Brian Bushnell</span></span>
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<td class="old_line diff-line-num old" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
6
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<td class="new_line diff-line-num old" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC6" class="line" lang="shell"><span class="s2" style="color: #d14;">Last modified <span class="idiff left deletion" style="background-color: #fac5cd;">Sept</span>ember <span class="idiff deletion" style="background-color: #fac5cd;">17</span>, 201<span class="idiff right deletion" style="background-color: #fac5cd;">8</span></span></span>
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<td class="old_line diff-line-num new" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
6
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC6" class="line" lang="shell"><span class="s2" style="color: #d14;">Last modified <span class="idiff left addition" style="background-color: #c7f0d2;">Dec</span>ember <span class="idiff addition" style="background-color: #c7f0d2;">22</span>, 20<span class="idiff right addition" style="background-color: #c7f0d2;">2</span>1</span></span>
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<td class="old_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
7
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<td class="new_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
7
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC7" class="line" lang="shell"><span class="s2" style="color: #d14;">This script requires at least 10GB RAM.</span></span>
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<td class="old_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
8
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<td class="new_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
8
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC8" class="line" lang="shell"><span class="s2" style="color: #d14;">It is designed for NERSC and uses hard-coded paths.</span></span>
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9
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<td class="new_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
9
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC9" class="line" lang="shell"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -73,7 +73,7 @@ calcXmx () {</td>
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73
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<td class="new_line diff-line-num" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
73
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC73" class="line" lang="shell">calcXmx <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$@</span><span class="s2" style="color: #d14;">"</span></span>
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74
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC74" class="line" lang="shell"></span>
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<td class="old_line diff-line-num" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
75
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<td class="new_line diff-line-num" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
75
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC75" class="line" lang="shell"><span class="k" style="font-weight: 600;">function </span>removemicrobes<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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<td class="new_line diff-line-num old" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC76" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">local </span><span class="nv" style="color: #008080;">CMD</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"java </span><span class="nv" style="color: #008080;">$EA</span><span class="s2" style="color: #d14;"> </span><span class="nv" style="color: #008080;">$EOOM</span><span class="s2" style="color: #d14;"> </span><span class="nv" style="color: #008080;">$z</span><span class="s2" style="color: #d14;"> </span><span class="nv" style="color: #008080;">$z2</span><span class="s2" style="color: #d14;"> </span><span class="nv" style="color: #008080;">$JNI</span><span class="s2" style="color: #d14;"> -cp </span><span class="nv" style="color: #008080;">$CP</span><span class="s2" style="color: #d14;"> align2.BBMap strictmaxindel=4 bwr=0.16 bw=12 ef=0.001 minhits=2 path=/global/<span class="idiff left right deletion" style="background-color: #fac5cd;">projectb/sandbox/gaag</span>/bbtools/commonMicrobes pigz unpigz zl=6 qtrim=r trimq=10 untrim idtag printunmappedcount ztd=2 kfilter=25 maxsites=1 k=13 minid=0.95 idfilter=0.95 minhits=2 build=1 bloomfilter </span><span class="nv" style="color: #008080;">$@</span><span class="s2" style="color: #d14;">"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
76
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC76" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">local </span><span class="nv" style="color: #008080;">CMD</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"java </span><span class="nv" style="color: #008080;">$EA</span><span class="s2" style="color: #d14;"> </span><span class="nv" style="color: #008080;">$EOOM</span><span class="s2" style="color: #d14;"> </span><span class="nv" style="color: #008080;">$z</span><span class="s2" style="color: #d14;"> </span><span class="nv" style="color: #008080;">$z2</span><span class="s2" style="color: #d14;"> </span><span class="nv" style="color: #008080;">$JNI</span><span class="s2" style="color: #d14;"> -cp </span><span class="nv" style="color: #008080;">$CP</span><span class="s2" style="color: #d14;"> align2.BBMap strictmaxindel=4 bwr=0.16 bw=12 ef=0.001 minhits=2 path=/global/<span class="idiff left right addition" style="background-color: #c7f0d2;">cfs/cdirs</span>/bbtools/commonMicrobes pigz unpigz zl=6 qtrim=r trimq=10 untrim idtag printunmappedcount ztd=2 kfilter=25 maxsites=1 k=13 minid=0.95 idfilter=0.95 minhits=2 build=1 bloomfilter </span><span class="nv" style="color: #008080;">$@</span><span class="s2" style="color: #d14;">"</span></span>
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77
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<td class="new_line diff-line-num" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
77
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC77" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$CMD</span> <span class="o" style="font-weight: 600;">></span>&2</span>
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<td class="old_line diff-line-num" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
78
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<td class="new_line diff-line-num" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
78
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC78" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">eval</span> <span class="nv" style="color: #008080;">$CMD</span></span>
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79
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC79" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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<a href="https://salsa.debian.org/med-team/bbmap/-/commit/1c662261847da712e5b04b94277f8aa712c37619#9f02f5242e6cef7d067a60833b9dcfe6d3692130" style="color: #1068bf; text-decoration: none;"><strong style="font-weight: bold;">resources/PacBioAdapter.fa</strong></a>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1" class="line" lang="plaintext">>PacBio_gDNA_Amplification_Adapter</span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC2" class="line" lang="plaintext">AAGCAGTGGTATCAACGCAGAGTACT</span></pre></td>
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<a href="https://salsa.debian.org/med-team/bbmap/-/commit/1c662261847da712e5b04b94277f8aa712c37619#3ceb66414e797c3aca775bd3535848b5bbdc22ba" style="color: #1068bf; text-decoration: none;"><strong style="font-weight: bold;">resources/contents.txt</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -82,3 +82,6 @@ These files contain consensus sequences of various conserved RNAs (rRNAs and tRN</td>
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82
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<td class="new_line diff-line-num" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
82
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC82" class="line" lang="plaintext">model.pgm</span>
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<td class="old_line diff-line-num" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
83
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<td class="new_line diff-line-num" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
83
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC83" class="line" lang="plaintext">Prokaryotic gene model, used by CallGenes and BBSketch in protein mode.</span>
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84
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84
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC84" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
85
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC85" class="line" lang="plaintext">PacBioAdapter.fa</span>
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<td class="new_line diff-line-num new" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
86
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC86" class="line" lang="plaintext">A sequence found at read tips in some PacBio low input libraries.</span>
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87
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC87" class="line" lang="plaintext"></span></pre></td>
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<a href="https://salsa.debian.org/med-team/bbmap/-/commit/1c662261847da712e5b04b94277f8aa712c37619#a7f35246a8c5f9ecfdce1ab90e6593332cb29506" style="color: #1068bf; text-decoration: none;"><strong style="font-weight: bold;">resources/short.fa</strong></a>
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<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -12,3 +12,10 @@ GTTCAGAGTTCTACAGTCCGACGATC</td>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC13" class="line" lang="plaintext">>contam_241</span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC14" class="line" lang="plaintext">TGGAATTCTCGGGTGCCAAGG</span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC15" class="line" lang="plaintext">>adapter_19mer_with_extensions</span>
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<a href="https://salsa.debian.org/med-team/bbmap/-/commit/1c662261847da712e5b04b94277f8aa712c37619#1465556c39c436e4247078a91cfda5084218249e" style="color: #1068bf; text-decoration: none;"><strong style="font-weight: bold;">shred.sh</strong></a>
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<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -3,7 +3,7 @@</td>
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<td class="old_line diff-line-num" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
3
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<td class="new_line diff-line-num" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
3
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC3" class="line" lang="shell">usage<span class="o" style="font-weight: 600;">(){</span></span>
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4
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<td class="new_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
4
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC4" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span></span>
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5
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<td class="new_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
5
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC5" class="line" lang="shell"><span class="s2" style="color: #d14;">Written by Brian Bushnell</span></span>
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<td class="old_line diff-line-num old" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
6
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<td class="new_line diff-line-num old" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC6" class="line" lang="shell"><span class="s2" style="color: #d14;">Last modified <span class="idiff left deletion" style="background-color: #fac5cd;">September</span> 1, 20<span class="idiff right deletion" style="background-color: #fac5cd;">16</span></span></span>
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<td class="new_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
6
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC6" class="line" lang="shell"><span class="s2" style="color: #d14;">Last modified <span class="idiff left addition" style="background-color: #c7f0d2;">January</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">3</span>, 20<span class="idiff right addition" style="background-color: #c7f0d2;">22</span></span></span>
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7
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<td class="new_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
7
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC7" class="line" lang="shell"><span class="s2" style="color: #d14;">Description: Shreds sequences into shorter, potentially overlapping sequences.</span></span>
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8
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<td class="new_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
8
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC8" class="line" lang="shell"></span>
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9
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<td class="new_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
9
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC9" class="line" lang="shell"><span class="s2" style="color: #d14;">Usage: shred.sh in=<file> out=<file> length=<number> minlength=<number> overlap=<number></span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -17,6 +17,7 @@ reads=-1 If nonnegative, stop after this many input sequences.</td>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC17" class="line" lang="shell"><span class="s2" style="color: #d14;">equal=f Shred each sequence into subsequences of equal size of at most 'length', instead of a fixed size.</span></span>
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<td class="old_line diff-line-num" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
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<td class="new_line diff-line-num" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC18" class="line" lang="shell"><span class="s2" style="color: #d14;">median=0 If nonzero, randomly shred reads to a length with this median.</span></span>
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<td class="old_line diff-line-num" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
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<td class="new_line diff-line-num" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
19
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC19" class="line" lang="shell"><span class="s2" style="color: #d14;">variance=0 If median is nonzero, shred to lengths of median +-variance.</span></span>
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<td class="old_line diff-line-num new" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC20" class="line" lang="shell"><span class="s2" style="color: #d14;">qfake=30 Quality score, if using fastq output.</span></span>
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<td class="new_line diff-line-num" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC21" class="line" lang="shell"></span>
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<td class="old_line diff-line-num" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
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<td class="new_line diff-line-num" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC22" class="line" lang="shell"><span class="s2" style="color: #d14;">Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.</span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC23" class="line" lang="shell"><span class="s2" style="color: #d14;">"</span></span>
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