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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/bbmap">Debian Med / bbmap</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/bbmap/commit/cad7edcb0ecb8c117a119a43641d19a4d072aa7e">cad7edcb</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-03-25T14:37:29Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add manpage
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bbmap/commit/8f5d9517e9395ffec2c29fa0c49818e8e8e7d722">8f5d9517</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-03-25T15:26:12Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Revert stripping .sh extension
</pre>
</li>
</ul>
<h4>7 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#bbad292d06faeeede4dff454112b59ccf45b0137">
<span class="new-file">
+
debian/bbmap.1
</span>
</a>
</li>
<li class="file-stats">
<a href="#33d1449847b6fd8a74bd14c46301bd0d12dafe62">
<span class="new-file">
+
debian/bbmap.links
</span>
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#ebcf9854ee19af4b7bf8405b283789c18769680f">
<span class="new-file">
+
debian/createmanpages
</span>
</a>
</li>
<li class="file-stats">
<a href="#efc7fe57b5983b0283c6410fceef7e74f687aeb5">
<span class="new-file">
+
debian/lintian-overrides
</span>
</a>
</li>
<li class="file-stats">
<a href="#68e0b13744e158347bfd74ebaaca667435f07d14">
<span class="new-file">
+
debian/manpages
</span>
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="bbad292d06faeeede4dff454112b59ccf45b0137">
<a href="https://salsa.debian.org/med-team/bbmap/compare/3af0c7e2ae7e8fa2bc6625074ffc8b53ef0ca72e...8f5d9517e9395ffec2c29fa0c49818e8e8e7d722#bbad292d06faeeede4dff454112b59ccf45b0137"><strong>debian/bbmap.1</strong></a>
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<td class="diff-line-num new new_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.8.</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH BBMAP "1" "March 2019" "bbmap 38.43" "User Commands"</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">.SH NAME</span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">bbmap \- Fast and accurate splice\-aware read aligner.</span>
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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH SYNOPSIS</span>
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">To index:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">.B bbmap.sh</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">ref=<reference fasta></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">.P</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">To map:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">.B bbmap.sh</span>
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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">in=<reads> out=<output sam></span>
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<td class="diff-line-num new new_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">.P</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">To map without writing an index:</span>
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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new new_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">.B bbmap.sh</span>
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<td class="diff-line-num new new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">ref=<reference fasta> in=<reads> out=<output sam> nodisk</span>
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<td class="diff-line-num new new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">.SH OPTIONS</span>
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<td class="diff-line-num new new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">in=stdin will accept reads from standard in, and out=stdout will write to</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">standard out, but file extensions are still needed to specify the format of the</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">input and output files e.g. in=stdin.fa.gz will read gzipped fasta from</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">standard in; out=stdout.sam.gz will write gzipped sam.</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">.SS Indexing Parameters (required when building the index):</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">.TP</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">nodisk=f</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">Set to true to build index in memory and write nothing</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">to disk except output.</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">.TP</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">ref=<file></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">Specify the reference sequence. Only do this ONCE,</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">when building the index (unless using 'nodisk').</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">.TP</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">build=1</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">If multiple references are indexed in the same directory,</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">each needs a unique numeric ID (unless using 'nodisk').</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">k=13</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">Kmer length, range 8\-15. Longer is faster but uses more memory.</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">Shorter is more sensitive.</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">If indexing and mapping are done in two steps, K should</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">be specified each time.</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">path=<.></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">Specify the location to write the index, if you don't</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">want it in the current working directory.</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">.TP</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">usemodulo=f</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">Throw away ~80% of kmers based on remainder modulo a</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">number (reduces RAM by 50% and sensitivity slightly).</span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">Should be enabled both when building the index AND</span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">when mapping.</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">.TP</span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">rebuild=f</span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">Force a rebuild of the index (ref= should be set).</span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">.SS Input Parameters:</span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">.TP</span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">build=1</span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">Designate index to use. Corresponds to the number</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">specified when building the index.</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">.TP</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">in=<file></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">Primary reads input; required parameter.</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">.TP</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">in2=<file></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">For paired reads in two files.</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext">.TP</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">interleaved=auto</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext">True forces paired/interleaved input; false forces</span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext">single\-ended mapping. If not specified, interleaved</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">status will be autodetected from read names.</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext">.TP</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext">fastareadlen=500</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext">Break up FASTA reads longer than this. Max is 500 for</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext">BBMap and 6000 for BBMapPacBio.</span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext">Only works for FASTA</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext">input (use 'maxlen' for FASTQ input).</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext">The default for</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext">\fBbbmap.sh\fR is 500, and for \fBmapPacBio.sh\fR is 6000.</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext">.TP</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext">unpigz=f</span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext">Spawn a pigz (parallel gzip) process for faster</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext">decompression than using Java.</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext">Requires pigz to be installed.</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext">.TP</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext">touppercase=t</span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext">(tuc) Convert lowercase letters in reads to upper case</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext">(otherwise they will not match the reference).</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext">.SS Sampling Parameters:</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext">.TP</span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext">reads=\-1</span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext">Set to a positive number N to only process the first N</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext">reads (or pairs), then quit.</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext">\fB\-1\fR means use all reads.</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext">.TP</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext">samplerate=1</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext">Set to a number from 0 to 1 to randomly select that</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext">fraction of reads for mapping. 1 uses all reads.</span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext">.TP</span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext">skipreads=0</span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext">Set to a number N to skip the first N reads (or pairs),</span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext">then map the rest.</span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext">.SS Mapping Parameters:</span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext">.TP</span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext">fast=f</span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext">This flag is a macro which sets other paramters to run</span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext">faster, at reduced sensitivity.</span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext">Bad for RNA\-seq.</span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext">.TP</span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext">slow=f</span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext">This flag is a macro which sets other paramters to run</span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext">slower, at greater sensitivity.</span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext">\&'vslow' is even slower.</span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext">.TP</span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext">maxindel=16000</span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext">Don't look for indels longer than this. Lower is faster.</span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext">.IP</span>
</pre>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext">Set to >=100k for RNAseq with long introns like mammals.</span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext">.TP</span>
</pre>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="plaintext">strictmaxindel=f</span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext">When enabled, do not allow indels longer than 'maxindel'.</span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext">.IP</span>
</pre>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="plaintext">By default these are not sought, but may be found anyway.</span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="plaintext">.TP</span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="plaintext">tipsearch=100</span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="plaintext">Look this far for read\-end deletions with anchors</span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="plaintext">shorter than K, using brute force.</span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="plaintext">.TP</span>
</pre>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="plaintext">minid=0.76</span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="plaintext">Approximate minimum alignment identity to look for.</span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="plaintext">.IP</span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext">Higher is faster and less sensitive.</span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="plaintext">.TP</span>
</pre>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="plaintext">minhits=1</span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="plaintext">Minimum number of seed hits required for candidate sites.</span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="plaintext">.IP</span>
</pre>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="plaintext">Higher is faster.</span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="plaintext">.TP</span>
</pre>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="plaintext">local=f</span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="plaintext">Set to true to use local, rather than global, alignments.</span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="plaintext">.IP</span>
</pre>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="plaintext">This will soft\-clip ugly ends of poor alignments.</span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="plaintext">.TP</span>
</pre>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="plaintext">perfectmode=f</span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="plaintext">Allow only perfect mappings when set to true (very fast).</span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="plaintext">.TP</span>
</pre>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="plaintext">semiperfectmode=f</span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="plaintext">Allow only perfect and semiperfect (perfect except for</span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="plaintext">N's in the reference) mappings.</span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="plaintext">.TP</span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="plaintext">threads=auto</span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="plaintext">(t) Set to number of threads desired. By default, uses</span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="plaintext">all cores available.</span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="plaintext">.TP</span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="plaintext">ambiguous=best</span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="plaintext">(ambig) Set behavior on ambiguously\-mapped reads (with</span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="plaintext">.IP</span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="plaintext">multiple top\-scoring mapping locations).</span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="plaintext">.IP</span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="plaintext">best (use the first best site)</span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="plaintext">.IP</span>
</pre>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="plaintext">toss (consider unmapped)</span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="plaintext">.IP</span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="plaintext">random (select one top\-scoring site randomly)</span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="plaintext">.IP</span>
</pre>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="plaintext">all (retain all top\-scoring sites)</span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="plaintext">.TP</span>
</pre>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="plaintext">samestrandpairs=f</span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="plaintext">(ssp) Specify whether paired reads should map to the</span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="plaintext">same strand or opposite strands.</span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="plaintext">.TP</span>
</pre>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="plaintext">requirecorrectstrand=t</span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="plaintext">(rcs) Forbid pairing of reads without correct strand</span>
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<td class="diff-line-num new new_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="plaintext">orientation.</span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="plaintext">.IP</span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="plaintext">Set to false for long\-mate\-pair libraries.</span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="plaintext">.TP</span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="plaintext">killbadpairs=f</span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="plaintext">(kbp) If a read pair is mapped with an inappropriate</span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="plaintext">insert size or orientation, the read with the lower</span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="plaintext">mapping quality is marked unmapped.</span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="plaintext">.TP</span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="plaintext">pairedonly=f</span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="plaintext">(po) Treat unpaired reads as unmapped. Thus they will</span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="plaintext">be sent to 'outu' but not 'outm'.</span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="plaintext">.TP</span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="plaintext">rcomp=f</span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="plaintext">Reverse complement both reads prior to mapping (for LMP</span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="plaintext">outward\-facing libraries).</span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="plaintext">.TP</span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="plaintext">rcompmate=f</span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="plaintext">Reverse complement read2 prior to mapping.</span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="plaintext">.TP</span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="plaintext">pairlen=32000</span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="plaintext">Set max allowed distance between paired reads.</span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="plaintext">.IP</span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="plaintext">(insert size)=(pairlen)+(read1 length)+(read2 length)</span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="plaintext">.TP</span>
</pre>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="plaintext">rescuedist=1200</span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="plaintext">Don't try to rescue paired reads if avg. insert size</span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="plaintext">greater than this.</span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="plaintext">Lower is faster.</span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="plaintext">.TP</span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="plaintext">rescuemismatches=32</span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="plaintext">Maximum mismatches allowed in a rescued read. Lower</span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="plaintext">is faster.</span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="plaintext">.TP</span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="plaintext">averagepairdist=100</span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="plaintext">(apd) Initial average distance between paired reads.</span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="plaintext">.IP</span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="plaintext">Varies dynamically; does not need to be specified.</span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="plaintext">.TP</span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="plaintext">deterministic=f</span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="plaintext">Run in deterministic mode. In this case it is good</span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="plaintext">to set averagepairdist.</span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="plaintext">BBMap is deterministic</span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="plaintext">without this flag if using single\-ended reads,</span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="plaintext">or run singlethreaded.</span>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="plaintext">.TP</span>
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222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="plaintext">bandwidthratio=0</span>
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223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="plaintext">(bwr) If above zero, restrict alignment band to this</span>
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224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="plaintext">fraction of read length.</span>
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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="plaintext">Faster but less accurate.</span>
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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="plaintext">.TP</span>
</pre>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="plaintext">bandwidth=0</span>
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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="plaintext">(bw) Set the bandwidth directly.</span>
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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="plaintext">fraction of read length.</span>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="plaintext">Faster but less accurate.</span>
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231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="plaintext">.TP</span>
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232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="plaintext">usejni=f</span>
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233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="plaintext">(jni) Do alignments faster, in C code.</span>
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234
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="plaintext">.TP</span>
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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="plaintext">maxsites2=800</span>
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236
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="plaintext">Don't analyze (or print) more than this many alignments</span>
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237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="plaintext">per read.</span>
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238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="plaintext">.TP</span>
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239
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="plaintext">ignorefrequentkmers=t</span>
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240
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="plaintext">(ifk) Discard low\-information kmers that occur often.</span>
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241
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="plaintext">.TP</span>
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242
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="plaintext">excludefraction=0.03</span>
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243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="plaintext">(ef) Fraction of kmers to ignore. For example, 0.03</span>
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244
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="plaintext">will ignore the most common 3% of kmers.</span>
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245
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="plaintext">.TP</span>
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246
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="plaintext">greedy=t</span>
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247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="plaintext">Use a greedy algorithm to discard the least\-useful</span>
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248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="plaintext">kmers on a per\-read basis.</span>
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249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="plaintext">.TP</span>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="plaintext">kfilter=0</span>
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251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="plaintext">If positive, potential mapping sites must have at</span>
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252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="plaintext">least this many consecutive exact matches.</span>
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253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="plaintext">.SS Quality and Trimming Parameters:</span>
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="plaintext">.TP</span>
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255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="plaintext">qin=auto</span>
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256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="plaintext">Set to 33 or 64 to specify input quality value ASCII</span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="plaintext">offset. 33 is Sanger, 64 is old Solexa.</span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="plaintext">.TP</span>
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259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="plaintext">qout=auto</span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="plaintext">Set to 33 or 64 to specify output quality value ASCII</span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="plaintext">offset (only if output format is fastq).</span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="plaintext">.TP</span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="plaintext">qtrim=f</span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="plaintext">Quality-trim ends before mapping. Options are:"</span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="plaintext">\&'f' (false), 'l' (left), 'r' (right), and 'lr' (both).</span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="plaintext">.TP</span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="plaintext">untrim=f</span>
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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="plaintext">Undo trimming after mapping. Untrimmed bases will be</span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="plaintext">soft\-clipped in cigar strings.</span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="plaintext">.TP</span>
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="plaintext">trimq=6</span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="plaintext">Trim regions with average quality below this</span>
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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="plaintext">(phred algorithm).</span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="plaintext">.TP</span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="plaintext">mintrimlength=60</span>
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="plaintext">(mintl) Don't trim reads to be shorter than this.</span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="plaintext">.TP</span>
</pre>
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278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="plaintext">fakefastaquality=\-1</span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="plaintext">(ffq) Set to a positive number 1\-50 to generate fake</span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="plaintext">quality strings for fasta input reads.</span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="plaintext">.TP</span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="plaintext">ignorebadquality=f</span>
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="plaintext">(ibq) Keep going, rather than crashing, if a read has</span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="plaintext">out\-of\-range quality values.</span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="plaintext">.TP</span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="plaintext">usequality=t</span>
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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="plaintext">Use quality scores when determining which read kmers</span>
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288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="plaintext">to use as seeds.</span>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="plaintext">.TP</span>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="plaintext">minaveragequality=0</span>
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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="plaintext">(maq) Do not map reads with average quality below this.</span>
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292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="plaintext">.TP</span>
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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="plaintext">maqb=0</span>
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294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="plaintext">If positive, calculate maq from this many initial bases.</span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="plaintext">.SS Output Parameters:</span>
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="plaintext">.TP</span>
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297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="plaintext">out=<file></span>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="plaintext">Write all reads to this file.</span>
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299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="plaintext">.TP</span>
</pre>
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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="plaintext">outu=<file></span>
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301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="plaintext">Write only unmapped reads to this file. Does not</span>
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302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="plaintext">include unmapped paired reads with a mapped mate.</span>
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303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="plaintext">.TP</span>
</pre>
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304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="plaintext">outm=<file></span>
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305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="plaintext">Write only mapped reads to this file. Includes</span>
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306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="plaintext">unmapped paired reads with a mapped mate.</span>
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307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="plaintext">.TP</span>
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308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="plaintext">mappedonly=f</span>
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309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="plaintext">If true, treats 'out' like 'outm'.</span>
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310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="plaintext">.TP</span>
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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="plaintext">bamscript=<file></span>
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312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="plaintext">(bs) Write a shell script to <file> that will turn</span>
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313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="plaintext">the sam output into a sorted, indexed bam file.</span>
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314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="plaintext">.TP</span>
</pre>
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315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="plaintext">ordered=f</span>
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316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="plaintext">Set to true to output reads in same order as input.</span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="plaintext">Slower and uses more memory.</span>
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318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="plaintext">.TP</span>
</pre>
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319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="plaintext">overwrite=f</span>
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="plaintext">(ow) Allow process to overwrite existing files.</span>
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321
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="plaintext">.TP</span>
</pre>
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322
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="plaintext">secondary=f</span>
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323
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="plaintext">Print secondary alignments.</span>
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324
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="plaintext">.TP</span>
</pre>
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325
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="plaintext">sssr=0.95</span>
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326
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="plaintext">(secondarysitescoreratio) Print only secondary alignments</span>
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327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="plaintext">with score of at least this fraction of primary.</span>
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328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="plaintext">.TP</span>
</pre>
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329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="plaintext">ssao=f</span>
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330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="plaintext">(secondarysiteasambiguousonly) Only print secondary</span>
</pre>
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331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="plaintext">alignments for ambiguously\-mapped reads.</span>
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332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="plaintext">.TP</span>
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333
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="plaintext">maxsites=5</span>
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334
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="plaintext">Maximum number of total alignments to print per read.</span>
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335
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="plaintext">Only relevant when secondary=t.</span>
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336
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="plaintext">.TP</span>
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337
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="plaintext">quickmatch=f</span>
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338
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="plaintext">Generate cigar strings more quickly.</span>
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339
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="plaintext">.TP</span>
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340
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="plaintext">trimreaddescriptions=f</span>
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341
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="plaintext">(trd) Truncate read and ref names at the first whitespace,</span>
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342
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="plaintext">assuming that the remainder is a comment or description.</span>
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343
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="plaintext">.TP</span>
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344
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="plaintext">ziplevel=2</span>
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345
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="plaintext">(zl) Compression level for zip or gzip output.</span>
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346
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="plaintext">.TP</span>
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347
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="plaintext">pigz=f</span>
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348
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="plaintext">Spawn a pigz (parallel gzip) process for faster</span>
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349
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="plaintext">compression than Java.</span>
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350
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="plaintext">.TP</span>
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351
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="plaintext">machineout=f</span>
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352
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="plaintext">Set to true to output statistics in machine\-friendly</span>
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353
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="plaintext">\&'key=value' format.</span>
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354
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="plaintext">.TP</span>
</pre>
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355
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="plaintext">printunmappedcount=f</span>
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356
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="plaintext">Print the total number of unmapped reads and bases.</span>
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357
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="plaintext">.IP</span>
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358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="plaintext">If input is paired, the number will be of pairs</span>
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359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="plaintext">for which both reads are unmapped.</span>
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360
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="plaintext">.TP</span>
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361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="plaintext">showprogress=0</span>
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362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="plaintext">If positive, print a '.' every X reads.</span>
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363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="plaintext">.TP</span>
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364
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="plaintext">showprogress2=0</span>
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365
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="plaintext">If positive, print the number of seconds since the</span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="plaintext">last progress update (instead of a '.').</span>
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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="plaintext">.TP</span>
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368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="plaintext">renamebyinsert=f</span>
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369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="plaintext">Renames reads based on their mapped insert size.</span>
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370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="plaintext">.SS Bloom\-Filtering Parameters (bloomfilter.sh is the standalone version).</span>
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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="plaintext">.TP</span>
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372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="plaintext">bloom=f</span>
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373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="plaintext">Use a Bloom filter to ignore reads not sharing kmers</span>
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374
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="plaintext">with the reference.</span>
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375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="plaintext">This uses more memory, but speeds</span>
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376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="plaintext">mapping when most reads don't match the reference.</span>
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377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="plaintext">.TP</span>
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378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="plaintext">bloomhashes=2</span>
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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="plaintext">Number of hash functions.</span>
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380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="plaintext">.TP</span>
</pre>
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381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="plaintext">bloomminhits=3</span>
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382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="plaintext">Number of consecutive hits to be considered matched.</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new new_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="plaintext">bloomk=31</span>
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<td class="diff-line-num new new_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="plaintext">Bloom filter kmer length.</span>
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<td class="diff-line-num new new_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="plaintext">.TP</span>
</pre>
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387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="plaintext">bloomserial=t</span>
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<td class="diff-line-num new new_line" data-linenumber="388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="plaintext">Use the serialized Bloom filter for greater loading</span>
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<td class="diff-line-num new new_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="plaintext">speed, if available.</span>
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<td class="diff-line-num new new_line" data-linenumber="390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="plaintext">If not, generate and write one.</span>
</pre>
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="plaintext">.SS Post\-Filtering Parameters:</span>
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<td class="diff-line-num new new_line" data-linenumber="392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="plaintext">.TP</span>
</pre>
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="plaintext">idfilter=0</span>
</pre>
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394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="plaintext">Independant of minid; sets exact minimum identity</span>
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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="plaintext">allowed for alignments to be printed.</span>
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396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="plaintext">Range 0 to 1.</span>
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397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="plaintext">.TP</span>
</pre>
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398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="plaintext">subfilter=\-1</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="plaintext">Ban alignments with more than this many substitutions.</span>
</pre>
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400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="plaintext">insfilter=\-1</span>
</pre>
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<td class="diff-line-num new new_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
402
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC402" class="line" lang="plaintext">Ban alignments with more than this many insertions.</span>
</pre>
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<td class="diff-line-num new new_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
403
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC403" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
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404
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="plaintext">delfilter=\-1</span>
</pre>
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<td class="diff-line-num new old_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
405
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="plaintext">Ban alignments with more than this many deletions.</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
406
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC406" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
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407
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="plaintext">indelfilter=\-1</span>
</pre>
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408
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="plaintext">Ban alignments with more than this many indels.</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
409
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
410
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="plaintext">editfilter=\-1</span>
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<td class="diff-line-num new new_line" data-linenumber="411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
411
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="plaintext">Ban alignments with more than this many edits.</span>
</pre>
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<td class="diff-line-num new new_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
412
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
413
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="plaintext">inslenfilter=\-1</span>
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<td class="diff-line-num new new_line" data-linenumber="414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
414
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC414" class="line" lang="plaintext">Ban alignments with an insertion longer than this.</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
415
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC415" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="416" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
416
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="plaintext">dellenfilter=\-1</span>
</pre>
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417
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC417" class="line" lang="plaintext">Ban alignments with a deletion longer than this.</span>
</pre>
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418
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="419" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
419
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="plaintext">nfilter=\-1</span>
</pre>
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420
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="plaintext">Ban alignments with more than this many ns. This</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="421" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
421
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="plaintext">includes nocall, noref, and off scaffold ends.</span>
</pre>
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422
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="plaintext">.SS Sam flags and settings:</span>
</pre>
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423
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="plaintext">.TP</span>
</pre>
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424
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="plaintext">noheader=f</span>
</pre>
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425
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="plaintext">Disable generation of header lines.</span>
</pre>
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426
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="plaintext">.TP</span>
</pre>
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427
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="plaintext">sam=1.4</span>
</pre>
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428
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="plaintext">Set to 1.4 to write Sam version 1.4 cigar strings,</span>
</pre>
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429
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="plaintext">with = and X, or 1.3 to use M.</span>
</pre>
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<td class="diff-line-num new new_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
430
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC430" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
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431
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="plaintext">saa=t</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="432" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
432
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC432" class="line" lang="plaintext">(secondaryalignmentasterisks) Use asterisks instead of</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="433" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
433
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="plaintext">bases for sam secondary alignments.</span>
</pre>
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434
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="plaintext">.TP</span>
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435
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="plaintext">cigar=t</span>
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436
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="plaintext">Set to 'f' to skip generation of cigar strings (faster).</span>
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437
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="plaintext">.TP</span>
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438
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="plaintext">keepnames=f</span>
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439
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="plaintext">Keep original names of paired reads, rather than</span>
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440
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="plaintext">ensuring both reads have the same name.</span>
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441
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="plaintext">.TP</span>
</pre>
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442
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="plaintext">intronlen=999999999</span>
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443
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="plaintext">Set to a lower number like 10 to change 'D' to 'N' in</span>
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444
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="plaintext">cigar strings for deletions of at least that length.</span>
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445
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="plaintext">.TP</span>
</pre>
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446
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="plaintext">rgid=</span>
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447
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="plaintext">Set readgroup ID. All other readgroup fields</span>
</pre>
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448
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="plaintext">can be set similarly, with the flag rgXX=</span>
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449
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="plaintext">.TP</span>
</pre>
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450
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="plaintext">mdtag=f</span>
</pre>
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451
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="plaintext">Write MD tags.</span>
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452
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="plaintext">.TP</span>
</pre>
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453
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="plaintext">nhtag=f</span>
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454
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="plaintext">Write NH tags.</span>
</pre>
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455
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="plaintext">.TP</span>
</pre>
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456
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="plaintext">xmtag=f</span>
</pre>
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457
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="plaintext">Write XM tags (may only work correctly with ambig=all).</span>
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458
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="plaintext">.TP</span>
</pre>
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459
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="plaintext">amtag=f</span>
</pre>
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460
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="plaintext">Write AM tags.</span>
</pre>
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461
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC461" class="line" lang="plaintext">.TP</span>
</pre>
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462
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="plaintext">nmtag=f</span>
</pre>
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<td class="diff-line-num new old_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
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463
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC463" class="line" lang="plaintext">Write NM tags.</span>
</pre>
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<td class="diff-line-num new old_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="464" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
464
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC464" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="465" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
465
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC465" class="line" lang="plaintext">xstag=f</span>
</pre>
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<td class="diff-line-num new old_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="466" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
466
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC466" class="line" lang="plaintext">Set to 'xs=fs', 'xs=ss', or 'xs=us' to write XS tags</span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="467" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
467
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC467" class="line" lang="plaintext">for RNAseq using firststrand, secondstrand, or</span>
</pre>
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<td class="diff-line-num new old_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="468" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
468
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC468" class="line" lang="plaintext">unstranded libraries. Needed by Cufflinks.</span>
</pre>
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469
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC469" class="line" lang="plaintext">JGI mainly uses 'firststrand'.</span>
</pre>
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<td class="diff-line-num new old_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="470" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
470
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC470" class="line" lang="plaintext">.TP</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="471" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
471
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC471" class="line" lang="plaintext">stoptag=f</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="472" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
472
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC472" class="line" lang="plaintext">Write a tag indicating read stop location, prefixed by YS:i:</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="473" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
473
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC473" class="line" lang="plaintext">.TP</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="474" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
474
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC474" class="line" lang="plaintext">lengthtag=f</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="475" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
475
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC475" class="line" lang="plaintext">Write a tag indicating (query,ref) alignment lengths,</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="476" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
476
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC476" class="line" lang="plaintext">prefixed by YL:Z:</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="477" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
477
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC477" class="line" lang="plaintext">.TP</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="478" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
478
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC478" class="line" lang="plaintext">idtag=f</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="479" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
479
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC479" class="line" lang="plaintext">Write a tag indicating percent identity, prefixed by YI:f:</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="480" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
480
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC480" class="line" lang="plaintext">.TP</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="481" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
481
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC481" class="line" lang="plaintext">inserttag=f</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="482" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
482
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC482" class="line" lang="plaintext">Write a tag indicating insert size, prefixed by X8:Z:</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="483" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
483
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC483" class="line" lang="plaintext">.TP</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="484" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
484
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC484" class="line" lang="plaintext">scoretag=f</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="485" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
485
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC485" class="line" lang="plaintext">Write a tag indicating BBMap's raw score, prefixed by YR:i:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="486" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
486
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="plaintext">.TP</span>
</pre>
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487
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="plaintext">timetag=f</span>
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488
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="plaintext">Write a tag indicating this read's mapping time, prefixed by X0:i:</span>
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489
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="plaintext">.TP</span>
</pre>
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490
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="plaintext">boundstag=f</span>
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<td class="diff-line-num new old_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="491" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
491
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="plaintext">Write a tag indicating whether either read in the pair</span>
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<td class="diff-line-num new new_line" data-linenumber="492" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
492
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC492" class="line" lang="plaintext">goes off the end of the reference, prefixed by XB:Z:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="493" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
493
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="494" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
494
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="plaintext">notags=f</span>
</pre>
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<td class="diff-line-num new old_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
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495
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="plaintext">Turn off all optional tags.</span>
</pre>
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496
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="plaintext">.SS Histogram and statistics output parameters:</span>
</pre>
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497
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
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498
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="plaintext">scafstats=<file></span>
</pre>
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<td class="diff-line-num new old_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
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499
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="plaintext">Statistics on how many reads mapped to which scaffold.</span>
</pre>
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500
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
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501
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="plaintext">refstats=<file></span>
</pre>
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<td class="diff-line-num new old_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
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502
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="plaintext">Statistics on how many reads mapped to which reference</span>
</pre>
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<td class="diff-line-num new old_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
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503
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="plaintext">file; only for BBSplit.</span>
</pre>
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504
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC504" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="505" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
505
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<pre style="margin: 0;">+<span id="LC505" class="line" lang="plaintext">sortscafs=t</span>
</pre>
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<td class="diff-line-num new old_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="506" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
506
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC506" class="line" lang="plaintext">Sort scaffolds or references by read count.</span>
</pre>
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<td class="diff-line-num new old_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="507" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
507
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC507" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
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508
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<pre style="margin: 0;">+<span id="LC508" class="line" lang="plaintext">bhist=<file></span>
</pre>
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<td class="diff-line-num new old_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="509" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
509
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC509" class="line" lang="plaintext">Base composition histogram by position.</span>
</pre>
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<td class="diff-line-num new old_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="510" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
510
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<pre style="margin: 0;">+<span id="LC510" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="511" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
511
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="plaintext">qhist=<file></span>
</pre>
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512
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="plaintext">Quality histogram by position.</span>
</pre>
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513
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<pre style="margin: 0;">+<span id="LC513" class="line" lang="plaintext">.TP</span>
</pre>
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514
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<pre style="margin: 0;">+<span id="LC514" class="line" lang="plaintext">aqhist=<file></span>
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<td class="diff-line-num new new_line" data-linenumber="515" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
515
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="plaintext">Histogram of average read quality.</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="516" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
516
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="plaintext">.TP</span>
</pre>
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517
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="plaintext">bqhist=<file></span>
</pre>
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518
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC518" class="line" lang="plaintext">Quality histogram designed for box plots.</span>
</pre>
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519
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC519" class="line" lang="plaintext">.TP</span>
</pre>
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520
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="plaintext">lhist=<file></span>
</pre>
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<td class="diff-line-num new old_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
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521
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC521" class="line" lang="plaintext">Read length histogram.</span>
</pre>
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522
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC522" class="line" lang="plaintext">.TP</span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
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523
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<pre style="margin: 0;">+<span id="LC523" class="line" lang="plaintext">ihist=<file></span>
</pre>
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524
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC524" class="line" lang="plaintext">Write histogram of insert sizes (for paired reads).</span>
</pre>
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525
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC525" class="line" lang="plaintext">.TP</span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
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526
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC526" class="line" lang="plaintext">ehist=<file></span>
</pre>
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527
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<pre style="margin: 0;">+<span id="LC527" class="line" lang="plaintext">Errors\-per\-read histogram.</span>
</pre>
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528
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC528" class="line" lang="plaintext">.TP</span>
</pre>
</td>
</tr>
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<td class="diff-line-num new old_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
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529
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC529" class="line" lang="plaintext">qahist=<file></span>
</pre>
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530
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC530" class="line" lang="plaintext">Quality accuracy histogram of error rates versus</span>
</pre>
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<td class="diff-line-num new old_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
531
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC531" class="line" lang="plaintext">quality score.</span>
</pre>
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<td class="diff-line-num new old_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
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532
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC532" class="line" lang="plaintext">.TP</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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533
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC533" class="line" lang="plaintext">indelhist=<file></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
534
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC534" class="line" lang="plaintext">Indel length histogram.</span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="535" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
535
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC535" class="line" lang="plaintext">.TP</span>
</pre>
</td>
</tr>
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<td class="diff-line-num new old_line" 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: 0 5px;" align="right" bgcolor="#ddfbe6">
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536
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC536" class="line" lang="plaintext">mhist=<file></span>
</pre>
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537
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="plaintext">Histogram of match, sub, del, and ins rates by</span>
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538
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<pre style="margin: 0;">+<span id="LC538" class="line" lang="plaintext">read location.</span>
</pre>
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539
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<pre style="margin: 0;">+<span id="LC539" class="line" lang="plaintext">.TP</span>
</pre>
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540
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<pre style="margin: 0;">+<span id="LC540" class="line" lang="plaintext">gchist=<file></span>
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541
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<pre style="margin: 0;">+<span id="LC541" class="line" lang="plaintext">Read GC content histogram.</span>
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542
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<pre style="margin: 0;">+<span id="LC542" class="line" lang="plaintext">.TP</span>
</pre>
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543
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<pre style="margin: 0;">+<span id="LC543" class="line" lang="plaintext">gcbins=100</span>
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544
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<pre style="margin: 0;">+<span id="LC544" class="line" lang="plaintext">Number gchist bins. Set to 'auto' to use read length.</span>
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545
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="plaintext">.TP</span>
</pre>
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546
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="plaintext">gcpairs=t</span>
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547
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<pre style="margin: 0;">+<span id="LC547" class="line" lang="plaintext">Use average GC of paired reads.</span>
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548
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<pre style="margin: 0;">+<span id="LC548" class="line" lang="plaintext">.TP</span>
</pre>
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549
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="plaintext">idhist=<file></span>
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550
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<pre style="margin: 0;">+<span id="LC550" class="line" lang="plaintext">Histogram of read count versus percent identity.</span>
</pre>
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551
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<pre style="margin: 0;">+<span id="LC551" class="line" lang="plaintext">.TP</span>
</pre>
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552
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<pre style="margin: 0;">+<span id="LC552" class="line" lang="plaintext">idbins=100</span>
</pre>
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553
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<pre style="margin: 0;">+<span id="LC553" class="line" lang="plaintext">Number idhist bins. Set to 'auto' to use read length.</span>
</pre>
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554
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<pre style="margin: 0;">+<span id="LC554" class="line" lang="plaintext">.TP</span>
</pre>
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555
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<pre style="margin: 0;">+<span id="LC555" class="line" lang="plaintext">statsfile=stderr</span>
</pre>
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556
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<pre style="margin: 0;">+<span id="LC556" class="line" lang="plaintext">Mapping statistics are printed here.</span>
</pre>
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557
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<pre style="margin: 0;">+<span id="LC557" class="line" lang="plaintext">.SS Coverage output parameters (these may reduce speed and use more RAM):</span>
</pre>
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558
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<pre style="margin: 0;">+<span id="LC558" class="line" lang="plaintext">.TP</span>
</pre>
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559
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="plaintext">covstats=<file></span>
</pre>
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560
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<pre style="margin: 0;">+<span id="LC560" class="line" lang="plaintext">Per\-scaffold coverage info.</span>
</pre>
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561
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<pre style="margin: 0;">+<span id="LC561" class="line" lang="plaintext">.TP</span>
</pre>
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562
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="plaintext">rpkm=<file></span>
</pre>
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563
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<pre style="margin: 0;">+<span id="LC563" class="line" lang="plaintext">Per\-scaffold RPKM/FPKM counts.</span>
</pre>
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564
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<pre style="margin: 0;">+<span id="LC564" class="line" lang="plaintext">.TP</span>
</pre>
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565
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<pre style="margin: 0;">+<span id="LC565" class="line" lang="plaintext">covhist=<file></span>
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566
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="plaintext">Histogram of # occurrences of each depth level.</span>
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567
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<pre style="margin: 0;">+<span id="LC567" class="line" lang="plaintext">.TP</span>
</pre>
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568
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<pre style="margin: 0;">+<span id="LC568" class="line" lang="plaintext">basecov=<file></span>
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569
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<pre style="margin: 0;">+<span id="LC569" class="line" lang="plaintext">Coverage per base location.</span>
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570
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<pre style="margin: 0;">+<span id="LC570" class="line" lang="plaintext">.TP</span>
</pre>
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571
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<pre style="margin: 0;">+<span id="LC571" class="line" lang="plaintext">bincov=<file></span>
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572
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<pre style="margin: 0;">+<span id="LC572" class="line" lang="plaintext">Print binned coverage per location (one line per X bases).</span>
</pre>
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573
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<pre style="margin: 0;">+<span id="LC573" class="line" lang="plaintext">.TP</span>
</pre>
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574
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<pre style="margin: 0;">+<span id="LC574" class="line" lang="plaintext">covbinsize=1000</span>
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575
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<pre style="margin: 0;">+<span id="LC575" class="line" lang="plaintext">Set the binsize for binned coverage output.</span>
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576
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<pre style="margin: 0;">+<span id="LC576" class="line" lang="plaintext">.TP</span>
</pre>
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577
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<pre style="margin: 0;">+<span id="LC577" class="line" lang="plaintext">nzo=t</span>
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578
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<pre style="margin: 0;">+<span id="LC578" class="line" lang="plaintext">Only print scaffolds with nonzero coverage.</span>
</pre>
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579
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<pre style="margin: 0;">+<span id="LC579" class="line" lang="plaintext">.TP</span>
</pre>
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580
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<pre style="margin: 0;">+<span id="LC580" class="line" lang="plaintext">twocolumn=f</span>
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581
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<pre style="margin: 0;">+<span id="LC581" class="line" lang="plaintext">Change to true to print only ID and Avg_fold instead of</span>
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582
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<pre style="margin: 0;">+<span id="LC582" class="line" lang="plaintext">all 6 columns to the 'out=' file.</span>
</pre>
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583
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<pre style="margin: 0;">+<span id="LC583" class="line" lang="plaintext">.TP</span>
</pre>
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584
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<pre style="margin: 0;">+<span id="LC584" class="line" lang="plaintext">32bit=f</span>
</pre>
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585
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<pre style="margin: 0;">+<span id="LC585" class="line" lang="plaintext">Set to true if you need per\-base coverage over 64k.</span>
</pre>
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586
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<pre style="margin: 0;">+<span id="LC586" class="line" lang="plaintext">.TP</span>
</pre>
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587
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<pre style="margin: 0;">+<span id="LC587" class="line" lang="plaintext">strandedcov=f</span>
</pre>
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588
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<pre style="margin: 0;">+<span id="LC588" class="line" lang="plaintext">Track coverage for plus and minus strand independently.</span>
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589
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<pre style="margin: 0;">+<span id="LC589" class="line" lang="plaintext">.TP</span>
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590
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<pre style="margin: 0;">+<span id="LC590" class="line" lang="plaintext">startcov=f</span>
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591
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<pre style="margin: 0;">+<span id="LC591" class="line" lang="plaintext">Only track start positions of reads.</span>
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592
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<pre style="margin: 0;">+<span id="LC592" class="line" lang="plaintext">.TP</span>
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593
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<pre style="margin: 0;">+<span id="LC593" class="line" lang="plaintext">secondarycov=t</span>
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594
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<pre style="margin: 0;">+<span id="LC594" class="line" lang="plaintext">Include coverage of secondary alignments.</span>
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595
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<pre style="margin: 0;">+<span id="LC595" class="line" lang="plaintext">.TP</span>
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596
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<pre style="margin: 0;">+<span id="LC596" class="line" lang="plaintext">physcov=f</span>
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597
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<pre style="margin: 0;">+<span id="LC597" class="line" lang="plaintext">Calculate physical coverage for paired reads.</span>
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598
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<pre style="margin: 0;">+<span id="LC598" class="line" lang="plaintext">This includes the unsequenced bases.</span>
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599
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<pre style="margin: 0;">+<span id="LC599" class="line" lang="plaintext">.TP</span>
</pre>
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600
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<pre style="margin: 0;">+<span id="LC600" class="line" lang="plaintext">delcoverage=t</span>
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601
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<pre style="margin: 0;">+<span id="LC601" class="line" lang="plaintext">(delcov) Count bases covered by deletions as covered.</span>
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602
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<pre style="margin: 0;">+<span id="LC602" class="line" lang="plaintext">True is faster than false.</span>
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603
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<pre style="margin: 0;">+<span id="LC603" class="line" lang="plaintext">.TP</span>
</pre>
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604
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<pre style="margin: 0;">+<span id="LC604" class="line" lang="plaintext">covk=0</span>
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605
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<pre style="margin: 0;">+<span id="LC605" class="line" lang="plaintext">If positive, calculate kmer coverage statistics.</span>
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606
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<pre style="margin: 0;">+<span id="LC606" class="line" lang="plaintext">.SS Java Parameters:</span>
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607
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<pre style="margin: 0;">+<span id="LC607" class="line" lang="plaintext">.TP</span>
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608
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<pre style="margin: 0;">+<span id="LC608" class="line" lang="plaintext">\fB\-Xmx\fR</span>
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609
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<pre style="margin: 0;">+<span id="LC609" class="line" lang="plaintext">This will set Java's memory usage,</span>
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610
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<pre style="margin: 0;">+<span id="LC610" class="line" lang="plaintext">overriding autodetection.</span>
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611
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<pre style="margin: 0;">+<span id="LC611" class="line" lang="plaintext">\fB\-Xmx20g\fR will specify 20 gigs of RAM, and \fB\-Xmx800m\fR</span>
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<td class="diff-line-num new new_line" data-linenumber="612" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
612
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<pre style="margin: 0;">+<span id="LC612" class="line" lang="plaintext">will specify 800 megs. The max is typically 85% of</span>
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613
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<pre style="margin: 0;">+<span id="LC613" class="line" lang="plaintext">physical memory. The human genome requires around 24g,</span>
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614
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<pre style="margin: 0;">+<span id="LC614" class="line" lang="plaintext">or 12g with the 'usemodulo' flag. The index uses</span>
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615
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<pre style="margin: 0;">+<span id="LC615" class="line" lang="plaintext">roughly 6 bytes per reference base.</span>
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616
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<pre style="margin: 0;">+<span id="LC616" class="line" lang="plaintext">.TP</span>
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617
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<pre style="margin: 0;">+<span id="LC617" class="line" lang="plaintext">\fB\-eoom\fR</span>
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618
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<pre style="margin: 0;">+<span id="LC618" class="line" lang="plaintext">This flag will cause the process to exit if an</span>
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619
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<pre style="margin: 0;">+<span id="LC619" class="line" lang="plaintext">out\-of\-memory exception occurs.</span>
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620
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<pre style="margin: 0;">+<span id="LC620" class="line" lang="plaintext">Requires Java 8u92+.</span>
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621
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<pre style="margin: 0;">+<span id="LC621" class="line" lang="plaintext">.TP</span>
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622
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<pre style="margin: 0;">+<span id="LC622" class="line" lang="plaintext">\fB\-da\fR</span>
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623
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<pre style="margin: 0;">+<span id="LC623" class="line" lang="plaintext">Disable assertions.</span>
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624
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<pre style="margin: 0;">+<span id="LC624" class="line" lang="plaintext">.SH SEE ALSO</span>
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625
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<pre style="margin: 0;">+<span id="LC625" class="line" lang="plaintext">Please read bbmap/docs/guides/BBMapGuide.txt for more information.</span>
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626
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<pre style="margin: 0;">+<span id="LC626" class="line" lang="plaintext">.SH AUTHOR</span>
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627
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<pre style="margin: 0;">+<span id="LC627" class="line" lang="plaintext">Written by Brian Bushnell, from Dec. 2010 \- present</span>
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628
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<pre style="margin: 0;">+<span id="LC628" class="line" lang="plaintext">.P</span>
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629
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<pre style="margin: 0;">+<span id="LC629" class="line" lang="plaintext">Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter</span>
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630
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<pre style="margin: 0;">+<span id="LC630" class="line" lang="plaintext">any problems, or post at: http://seqanswers.com/forums/showthread.php?t=41057</span>
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631
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<pre style="margin: 0;">+<span id="LC631" class="line" lang="plaintext">.P</span>
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632
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<pre style="margin: 0;">+<span id="LC632" class="line" lang="plaintext">This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.</span></pre>
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<li id="33d1449847b6fd8a74bd14c46301bd0d12dafe62">
<a href="https://salsa.debian.org/med-team/bbmap/compare/3af0c7e2ae7e8fa2bc6625074ffc8b53ef0ca72e...8f5d9517e9395ffec2c29fa0c49818e8e8e7d722#33d1449847b6fd8a74bd14c46301bd0d12dafe62"><strong>debian/bbmap.links</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">usr/lib/debian-med/bin/bbmap.sh usr/bin/bbmap.sh</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">usr/lib/debian-med/bin/bloomfilter.sh usr/bin/bloomfilter.sh</span></pre>
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<a href="https://salsa.debian.org/med-team/bbmap/compare/3af0c7e2ae7e8fa2bc6625074ffc8b53ef0ca72e...8f5d9517e9395ffec2c29fa0c49818e8e8e7d722#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6,7 +6,8 @@ Priority: optional</td>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="mosel"><span class="n" style="color: #333;">Build</span><span class="p">-</span><span class="n" style="color: #333;">Depends</span><span class="p">:</span> <span class="n" style="color: #333;">debhelper</span> <span class="p">(>=</span> <span class="m" style="color: #099;">12</span><span class="p">~),</span></span>
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7
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="mosel"> <span class="n" style="color: #333;">javahelper</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="mosel"> <span class="n" style="color: #333;">default</span><span class="p">-</span><span class="n" style="color: #333;">jdk</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="mosel"> <span class="n" style="color: #333;">libmpj</span><span class="p">-</span><span class="n" style="color: #333;">java</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="mosel"> <span class="n" style="color: #333;">libmpj</span><span class="p">-</span><span class="n" style="color: #333;">java</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="mosel"> <span class="n" style="color: #333;">rename</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="mosel"><span class="n" style="color: #333;">Standards</span><span class="p">-</span><span class="k" style="font-weight: 600;">Version</span><span class="p">:</span> <span class="m" style="color: #099;">4.3.0</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="mosel"><span class="n" style="color: #333;">Vcs</span><span class="p">-</span><span class="n" style="color: #333;">Browser</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">salsa</span><span class="p">.</span><span class="n" style="color: #333;">debian</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">med</span><span class="p">-</span><span class="n" style="color: #333;">team</span><span class="p">/</span><span class="n" style="color: #333;">bbmap</span></span>
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12
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="mosel"><span class="n" style="color: #333;">Vcs</span><span class="p">-</span><span class="n" style="color: #333;">Git</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">salsa</span><span class="p">.</span><span class="n" style="color: #333;">debian</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">med</span><span class="p">-</span><span class="n" style="color: #333;">team</span><span class="p">/</span><span class="n" style="color: #333;">bbmap</span><span class="p">.</span><span class="n" style="color: #333;">git</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -16,6 +17,7 @@ Package: bbmap</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="mosel"><span class="n" style="color: #333;">Architecture</span><span class="p">:</span> <span class="n" style="color: #333;">all</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="mosel"><span class="n" style="color: #333;">Depends</span><span class="p">:</span> <span class="p">${</span><span class="n" style="color: #333;">java</span><span class="p">:</span><span class="n" style="color: #333;">Depends</span><span class="p">},</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="mosel"> <span class="p">${</span><span class="n" style="color: #333;">misc</span><span class="p">:</span><span class="n" style="color: #333;">Depends</span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="mosel"><span class="n" style="color: #333;">Recommends</span><span class="p">:</span> <span class="n" style="color: #333;">pigz</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="mosel"><span class="n" style="color: #333;">Description</span><span class="p">:</span> <span class="n" style="color: #333;">short</span> <span class="nb" style="color: #0086b3;">read</span> <span class="n" style="color: #333;">aligner</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">other</span> <span class="n" style="color: #333;">bioinformatic</span> <span class="n" style="color: #333;">tools</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="mosel"> <span class="n" style="color: #333;">BBMap</span><span class="p">:</span> <span class="n" style="color: #333;">Short</span> <span class="nb" style="color: #0086b3;">read</span> <span class="n" style="color: #333;">aligner</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">DNA</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">RNA</span><span class="p">-</span><span class="n" style="color: #333;">seq</span> <span class="n" style="color: #333;">data</span><span class="p">.</span> <span class="n" style="color: #333;">Capable</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">handling</span></span>
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<td class="diff-line-num new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="mosel"> <span class="n" style="color: #333;">arbitrarily</span> <span class="n" style="color: #333;">large</span> <span class="n" style="color: #333;">genomes</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">millions</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">scaffolds</span><span class="p">.</span> <span class="n" style="color: #333;">Handles</span> <span class="n" style="color: #333;">Illumina</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -46,5 +48,5 @@ Description: short read aligner and other bioinformatic tools - JNI library</td>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="mosel"> <span class="n" style="color: #333;">PacBio</span><span class="p">,</span> <span class="m" style="color: #099;">454</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">other</span> <span class="n" style="color: #333;">reads</span><span class="p">;</span> <span class="n" style="color: #333;">very</span> <span class="n" style="color: #333;">high</span> <span class="n" style="color: #333;">sensitivity</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">tolerant</span> <span class="k" style="font-weight: 600;">of</span></span>
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<td class="diff-line-num new_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="mosel"> <span class="n" style="color: #333;">errors</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">numerous</span> <span class="n" style="color: #333;">large</span> <span class="n" style="color: #333;">indels</span><span class="p">.</span></span>
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48
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="mosel"> <span class="p">.</span></span>
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<td class="diff-line-num new_line old" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="mosel"> <span class="n" style="color: #333;">This</span> <span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">contains</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">architecture</span> <span class="n" style="color: #333;">depend<span class="idiff left right">e</span>nt</span> <span class="n" style="color: #333;">library</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">bbmap</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="mosel"> <span class="n" style="color: #333;">This</span> <span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">contains</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">architecture</span> <span class="n" style="color: #333;">depend<span class="idiff left right">a</span>nt</span> <span class="n" style="color: #333;">library</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">bbmap</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="mosel"> <span class="n" style="color: #333;">tools</span><span class="p">.</span></span></pre>
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<a href="https://salsa.debian.org/med-team/bbmap/compare/3af0c7e2ae7e8fa2bc6625074ffc8b53ef0ca72e...8f5d9517e9395ffec2c29fa0c49818e8e8e7d722#ebcf9854ee19af4b7bf8405b283789c18769680f"><strong>debian/createmanpages</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/sh</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="nv" style="color: teal;">MANDIR</span><span class="o" style="font-weight: 600;">=</span>debian</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: navy;">-p</span> <span class="nv" style="color: teal;">$MANDIR</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="nv" style="color: teal;">VERSION</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span>dpkg-parsechangelog | <span class="nb" style="color: #0086b3;">awk</span> <span class="s1" style="color: #d14;">'/^Version:/ {print $2}'</span> | <span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'s/^[0-9]*://'</span> <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'s/-.*//'</span> <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'s/[+~]dfsg$//'</span><span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="nv" style="color: teal;">NAME</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">grep</span> <span class="s2" style="color: #d14;">"^Description:"</span> debian/control | <span class="nb" style="color: #0086b3;">sed</span> <span class="s1" style="color: #d14;">'s/^Description: *//'</span> | <span class="nb" style="color: #0086b3;">head</span> <span class="nt" style="color: navy;">-n1</span><span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="nv" style="color: teal;">PROGNAME</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">grep</span> <span class="s2" style="color: #d14;">"^Package:"</span> debian/control | <span class="nb" style="color: #0086b3;">sed</span> <span class="s1" style="color: #d14;">'s/^Package: *//'</span> | <span class="nb" style="color: #0086b3;">head</span> <span class="nt" style="color: navy;">-n1</span><span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="nv" style="color: teal;">AUTHOR</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">".SH AUTHOR</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">This manpage was written by </span><span class="nv" style="color: teal;">$DEBFULLNAME</span><span class="s2" style="color: #d14;"> for the Debian distribution and</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="s2" style="color: #d14;">can be used for any other usage of the program.</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># If program name is different from package name or title should be</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># different from package short description change this here</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="nv" style="color: teal;">progname</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">PROGNAME</span><span class="k" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell">help2man <span class="nt" style="color: navy;">--no-info</span> <span class="nt" style="color: navy;">--no-discard-stderr</span> <span class="nt" style="color: navy;">--help-option</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">" "</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"> <span class="nt" style="color: navy;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$NAME</span><span class="s2" style="color: #d14;">"</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"> <span class="nt" style="color: navy;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">progname</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: teal;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: teal;">$AUTHOR</span> <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: teal;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$MANDIR</span><span class="s2" style="color: #d14;">/*.1"</span> <span class="o" style="font-weight: 600;">></span> debian/manpages</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat</span> <span class="o" style="font-weight: 600;"><<</span><span class="no" style="color: teal;">EOT</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"><span class="sh" style="color: #d14;">Please enhance the help2man output.</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"><span class="sh" style="color: #d14;">The following web page might be helpful in doing so:</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"><span class="sh" style="color: #d14;"> http://liw.fi/manpages/</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"><span class="no" style="color: teal;">EOT</span></span></pre>
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<a href="https://salsa.debian.org/med-team/bbmap/compare/3af0c7e2ae7e8fa2bc6625074ffc8b53ef0ca72e...8f5d9517e9395ffec2c29fa0c49818e8e8e7d722#efc7fe57b5983b0283c6410fceef7e74f687aeb5"><strong>debian/lintian-overrides</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"># see https://lists.debian.org/debian-med/2018/06/msg00043.html</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">bbmap: script-with-language-extension usr/bin/*.*</span></pre>
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<a href="https://salsa.debian.org/med-team/bbmap/compare/3af0c7e2ae7e8fa2bc6625074ffc8b53ef0ca72e...8f5d9517e9395ffec2c29fa0c49818e8e8e7d722#68e0b13744e158347bfd74ebaaca667435f07d14"><strong>debian/manpages</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/*.1</span></pre>
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<a href="https://salsa.debian.org/med-team/bbmap/compare/3af0c7e2ae7e8fa2bc6625074ffc8b53ef0ca72e...8f5d9517e9395ffec2c29fa0c49818e8e8e7d722#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -34,10 +34,14 @@ override_dh_install:</td>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"> if [ "$${scr}" != "calcmem.sh" ] ; then \</span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext"> sed -e 's:^CP=".DIR""current/":CP=/usr/share/java/bbmap.jar:' \</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext"> -e 's:source ".DIR""/calcmem.sh":source "/usr/share/$(DEB_SOURCE)/calcmem":' \</span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="plaintext"> $${scr} > $(PKGBINDIR)/<span class="idiff left right">`basename $${scr} .sh`</span> ; \</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> $${scr} > $(PKGBINDIR)/<span class="idiff left right">$${scr}</span> ; \</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext"> fi ; \</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext"> done</span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext">override_dh_fixperms:</span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext"> dh_fixperms</span>
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43
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext"> chmod +x $(PKGBINDIR)/*</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">override_dh_installman:</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"> dh_installman</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"> rename 's/\.1$$/.sh.1/' debian/$(DEB_SOURCE)/usr/share/man/man1/*.1</span></pre>
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