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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/chip-seq">Debian Med / chip-seq</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/chip-seq/-/commit/04e596b861be1bb32bbd0aa3b52ee0b2b70246f7">04e596b8</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-03-26T16:27:26+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add missing Depends
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/chip-seq/-/commit/064880d33721dd2a4bf008fd0802c1b064dee34a">064880d3</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-03-26T16:33:20+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">More manpages
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/chip-seq/-/commit/a26569d2eb5b4ce2d9c2e92ec8f8a2776bea4873">a26569d2</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-03-26T16:34:46+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Create data package since the data are actually used.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/chip-seq/-/commit/b538d7a42d2fac928d07113a5daa9dc2c7a9093a">b538d7a4</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-03-26T16:44:50+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adapt database installation PATH to Debian location
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/chip-seq/-/commit/923b8372971690e2ac22d4f3a94a7d581a04eec9">923b8372</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-03-26T16:53:55+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix installation of usr/bin and some *.pl manpages
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/chip-seq/-/commit/d69d1c535a6fc706d44e040e63f506b640ed9b22">d69d1c53</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-03-26T16:56:26+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Enhance description
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/chip-seq/-/commit/29c107c4a7129017c165559b8b8ecba53afd3314">29c107c4</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-03-26T16:57:57+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix permissions
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/chip-seq/-/commit/ee6a173ffb1d2385a5a14e029dc0968af570f43d">ee6a173f</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-03-26T17:01:39+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Some more manpages
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/chip-seq/-/commit/5c1c219674ea08aaf558f4c88a3a52e40719e5ce">5c1c2196</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-03-26T17:04:23+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fif dh_fixperms
</pre>
</li>
</ul>
<h4>24 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#d6af915c334542648830e33da3390229e832b3ea">
<span class="new-file">
+
debian/chip-seq-data.install
</span>
</a>
</li>
<li class="file-stats">
<a href="#306c5f7917f792cd491741195bfa360224870708">
debian/examples
→
debian/chip-seq.examples
</a>
</li>
<li class="file-stats">
<a href="#a5c78e35fcfffdffcf6e6ccb3dff92b540295272">
<span class="new-file">
+
debian/chip-seq.install
</span>
</a>
</li>
<li class="file-stats">
<a href="#35efd9c0b880828631e13f5265ad6874ff87d40c">
debian/lintian-overrides
→
debian/chip-seq.lintian-overrides
</a>
</li>
<li class="file-stats">
<a href="#083d04a8986398644e19118e71acfc541c923108">
<span class="new-file">
+
debian/chip-seq.manpages
</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="#68e0b13744e158347bfd74ebaaca667435f07d14">
<span class="deleted-file">
−
debian/manpages
</span>
</a>
</li>
<li class="file-stats">
<a href="#406d10df774ee8ef1b46900b89f07a8dabc751a9">
<span class="new-file">
+
debian/mans/bed2bed_display.1
</span>
</a>
</li>
<li class="file-stats">
<a href="#ba0e772a2b58bfe82d22bbbb80343c8740ebab9a">
<span class="new-file">
+
debian/mans/bed2sga.1
</span>
</a>
</li>
<li class="file-stats">
<a href="#37296ab03814e440a642152108e8e3be70fdd549">
<span class="new-file">
+
debian/mans/compactsga.1
</span>
</a>
</li>
<li class="file-stats">
<a href="#27f4fb020354d6d3056ff8281ab8e61c7c7a87cd">
<span class="new-file">
+
debian/mans/countsga.1
</span>
</a>
</li>
<li class="file-stats">
<a href="#4e4a2cf6f450babce42b27ec34be504e9d4de33a">
<span class="new-file">
+
debian/mans/featreplace.1
</span>
</a>
</li>
<li class="file-stats">
<a href="#e52ff9008ba9438986bc2b3c47e61a6e0eef5bcc">
<span class="new-file">
+
debian/mans/filter_counts.1
</span>
</a>
</li>
<li class="file-stats">
<a href="#e86578b0d1dbef8f60921d329b45f6d79bc3345b">
<span class="new-file">
+
debian/mans/fps2sga.pl.1
</span>
</a>
</li>
<li class="file-stats">
<a href="#96ff0c1a27b68a94a0bc4e272c2df80c2e26a6f4">
<span class="new-file">
+
debian/mans/gff2sga.pl.1
</span>
</a>
</li>
<li class="file-stats">
<a href="#b9a4899642c1c76fbabf5d82080be8de13d0b016">
<span class="new-file">
+
debian/mans/partit2bed.pl.1
</span>
</a>
</li>
<li class="file-stats">
<a href="#58d99a432a997aa43330a4bdeb9e028feb358a4a">
<span class="new-file">
+
debian/mans/sga2bed.1
</span>
</a>
</li>
<li class="file-stats">
<a href="#f56abfaa2778699e2bfc82e6d68c1ac1678f1048">
<span class="new-file">
+
debian/mans/sga2fps.pl.1
</span>
</a>
</li>
<li class="file-stats">
<a href="#0c6939d517692a3ad80e2549605b22c77851e168">
<span class="new-file">
+
debian/mans/sga2gff.pl.1
</span>
</a>
</li>
<li class="file-stats">
<a href="#306ad0e42c6d098ddeb6d6d7db32c47f84689c7f">
<span class="new-file">
+
debian/mans/sga2wig.1
</span>
</a>
</li>
<li class="file-stats">
<a href="#91629de237e1cfa7686ea02d3c8ee710c369ec8b">
<span class="new-file">
+
debian/patches/data_location.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="d6af915c334542648830e33da3390229e832b3ea">
<a href="https://salsa.debian.org/med-team/chip-seq/-/compare/340f7777e3fe3f28dc5c46e996d0b6d63ccb2411...5c1c219674ea08aaf558f4c88a3a52e40719e5ce#d6af915c334542648830e33da3390229e832b3ea"><strong>debian/chip-seq-data.install</strong></a>
<hr>
<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="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="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nx">share</span><span class="o" style="font-weight: 600;">/*</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">chip</span><span class="o" style="font-weight: 600;">-</span><span class="nx">seq</span></span></pre>
</td>
</tr>
</table>
<br>
</li>
<li id="306c5f7917f792cd491741195bfa360224870708">
<a href="https://salsa.debian.org/med-team/chip-seq/-/compare/340f7777e3fe3f28dc5c46e996d0b6d63ccb2411...5c1c219674ea08aaf558f4c88a3a52e40719e5ce#306c5f7917f792cd491741195bfa360224870708"><strong>debian/examples</strong>
→
<strong>debian/chip-seq.examples</strong>
</a>
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<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">
</table>
<br>
</li>
<li id="a5c78e35fcfffdffcf6e6ccb3dff92b540295272">
<a href="https://salsa.debian.org/med-team/chip-seq/-/compare/340f7777e3fe3f28dc5c46e996d0b6d63ccb2411...5c1c219674ea08aaf558f4c88a3a52e40719e5ce#a5c78e35fcfffdffcf6e6ccb3dff92b540295272"><strong>debian/chip-seq.install</strong></a>
<hr>
<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="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="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span></span></pre>
</td>
</tr>
</table>
<br>
</li>
<li id="35efd9c0b880828631e13f5265ad6874ff87d40c">
<a href="https://salsa.debian.org/med-team/chip-seq/-/compare/340f7777e3fe3f28dc5c46e996d0b6d63ccb2411...5c1c219674ea08aaf558f4c88a3a52e40719e5ce#35efd9c0b880828631e13f5265ad6874ff87d40c"><strong>debian/lintian-overrides</strong>
→
<strong>debian/chip-seq.lintian-overrides</strong>
</a>
<hr>
<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">
</table>
<br>
</li>
<li id="083d04a8986398644e19118e71acfc541c923108">
<a href="https://salsa.debian.org/med-team/chip-seq/-/compare/340f7777e3fe3f28dc5c46e996d0b6d63ccb2411...5c1c219674ea08aaf558f4c88a3a52e40719e5ce#083d04a8986398644e19118e71acfc541c923108"><strong>debian/chip-seq.manpages</strong></a>
<hr>
<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="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="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">*1.gz</span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="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="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">debian/mans/*.1</span></pre>
</td>
</tr>
</table>
<br>
</li>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/chip-seq/-/compare/340f7777e3fe3f28dc5c46e996d0b6d63ccb2411...5c1c219674ea08aaf558f4c88a3a52e40719e5ce#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
<hr>
<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -12,7 +12,9 @@ Homepage: https://ccg.epfl.ch//chipseq</td>
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<td class="diff-line-num old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
12
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<td class="diff-line-num new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Package: chip-seq</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Architecture: any</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="diff-line-num new_line old" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"> ${misc:Depends}</span>
</pre>
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<td class="diff-line-num new old_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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<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"> ${misc:Depends},</span>
</pre>
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<td class="diff-line-num new old_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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<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"> chip-seq-data,</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> libmath-round-perl</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Description: tools performing common ChIP-Seq data analysis tasks</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> The ChIP-Seq software provides a set of tools performing common genome-</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> wide ChIP- seq analysis tasks, including positional correlation</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -33,3 +35,29 @@ Description: tools performing common ChIP-Seq data analysis tasks</td>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext"> their own compact format for ChIP-seq data representation called SGA</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext"> (Simplified Genome Annotation). SGA is a line-oriented, tab-delimited</span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext"> plain text format.</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">Package: chip-seq-data</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">Depends: ${misc:Depends}</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">Description: tools performing common ChIP-Seq data analysis tasks (data)</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"> The ChIP-Seq software provides a set of tools performing common genome-</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"> wide ChIP- seq analysis tasks, including positional correlation</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"> analysis, peak detection, and genome partitioning into signal-rich and</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"> signal-poor regions. These tools exist as stand-alone C programs and</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"> perform the following tasks:</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"> 1. Positional correlation analysis and generation of an aggregation</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"> plot (AP) (chipcor),</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"> 2. Extraction of specific genome annotation features around reference</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"> anchor points (chipextract),</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"> 3. Read centering or shifting (chipcenter),</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext"> 4. Narrow peak caller using a fixed width peak size (chippeak),</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext"> 5. Broad peak caller used for large regions of enrichment (chippart),</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext"> 6. Feature selection tool based on a read count threshold (chipscore).</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext"> Because the ChIP-Seq tools are primarily optimized for speed, they use</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext"> their own compact format for ChIP-seq data representation called SGA</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext"> (Simplified Genome Annotation). SGA is a line-oriented, tab-delimited</span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"> plain text format.</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext"> This package contains the database files shipped with chip-seq.</span></pre>
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<a href="https://salsa.debian.org/med-team/chip-seq/-/compare/340f7777e3fe3f28dc5c46e996d0b6d63ccb2411...5c1c219674ea08aaf558f4c88a3a52e40719e5ce#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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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="nv" style="color: #008080;">MANDIR</span><span class="o" style="font-weight: 600;">=</span>debian/mans</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: #000080;">-p</span> <span class="nv" style="color: #008080;">$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: #008080;">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 $2}'</span> | <span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/^[0-9]*://'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/-.*//'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/[+~]dfsg$//'</span><span class="sb" style="color: #d14;">`</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="nv" style="color: #008080;">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: #000080;">-n1</span><span class="sb" style="color: #d14;">`</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="nv" style="color: #008080;">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: #000080;">-n1</span><span class="sb" style="color: #d14;">`</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="nv" style="color: #008080;">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;"> </span><span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="s2" style="color: #d14;">This manpage was written by </span><span class="nv" style="color: #008080;">$DEBFULLNAME</span><span class="s2" style="color: #d14;"> for the Debian distribution and</span><span class="se" style="color: #d14;">\n</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="LC11" class="line" lang="shell"><span class="s2" style="color: #d14;">can be used for any other usage of the program.</span><span class="se" style="color: #d14;">\</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="s2" style="color: #d14;">"</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"></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;"># If program name is different from package name or title should be</span></span>
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<pre style="margin: 0;">+<span id="LC15" 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="LC16" class="line" lang="shell"><span class="nv" style="color: #008080;">progname</span><span class="o" style="font-weight: 600;">=</span>bed2bed_display</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell">help2man <span class="nt" style="color: #000080;">--no-info</span> <span class="nt" style="color: #000080;">--no-discard-stderr</span> <span class="nt" style="color: #000080;">--help-option</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">" -h"</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: #000080;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"Convert BED file to BED format suitable for displaying ChIP-seq peaks."</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"> <span class="nt" style="color: #000080;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$AUTHOR</span> <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"><span class="nv" style="color: #008080;">progname</span><span class="o" style="font-weight: 600;">=</span>bed2sga</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell">help2man <span class="nt" style="color: #000080;">--no-info</span> <span class="nt" style="color: #000080;">--no-discard-stderr</span> <span class="nt" style="color: #000080;">--help-option</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">" -h"</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"> <span class="nt" style="color: #000080;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"Convert BED format into SGA format."</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"> <span class="nt" style="color: #000080;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$AUTHOR</span> <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Provided upstream:</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># chipcenter</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># chipcor</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># chipextract</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># chippart</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># chippeak</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># chipscore</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell"><span class="nv" style="color: #008080;">progname</span><span class="o" style="font-weight: 600;">=</span>compactsga</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell">help2man <span class="nt" style="color: #000080;">--no-info</span> <span class="nt" style="color: #000080;">--no-discard-stderr</span> <span class="nt" style="color: #000080;">--help-option</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">" -h"</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="shell"> <span class="nt" style="color: #000080;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"reads a ChIP-seq data file and merges equal tag positions into a single line"</span> <span class="se" style="color: #d14;">\</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="shell"> <span class="nt" style="color: #000080;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$AUTHOR</span> <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="shell"></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="shell"><span class="nv" style="color: #008080;">progname</span><span class="o" style="font-weight: 600;">=</span>countsga</span>
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<td class="diff-line-num new new_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="shell">help2man <span class="nt" style="color: #000080;">--no-info</span> <span class="nt" style="color: #000080;">--no-discard-stderr</span> <span class="nt" style="color: #000080;">--help-option</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">" -h"</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="shell"> <span class="nt" style="color: #000080;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"read a ChIP-seq data file and computes the total number of tag counts"</span> <span class="se" style="color: #d14;">\</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="shell"> <span class="nt" style="color: #000080;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$AUTHOR</span> <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="shell"></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="shell"><span class="nv" style="color: #008080;">progname</span><span class="o" style="font-weight: 600;">=</span>featreplace</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="shell">help2man <span class="nt" style="color: #000080;">--no-info</span> <span class="nt" style="color: #000080;">--no-discard-stderr</span> <span class="nt" style="color: #000080;">--help-option</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">" -h"</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="shell"> <span class="nt" style="color: #000080;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"read a ChIP-seq data file and changes the name of the feature field"</span> <span class="se" style="color: #d14;">\</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="shell"> <span class="nt" style="color: #000080;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$AUTHOR</span> <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="shell"></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="shell"><span class="nv" style="color: #008080;">progname</span><span class="o" style="font-weight: 600;">=</span>filter_counts</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="shell">help2man <span class="nt" style="color: #000080;">--no-info</span> <span class="nt" style="color: #000080;">--no-discard-stderr</span> <span class="nt" style="color: #000080;">--help-option</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">" -h"</span> <span class="se" style="color: #d14;">\</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="shell"> <span class="nt" style="color: #000080;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"read a ChIP-seq data file and filters out all read counts"</span> <span class="se" style="color: #d14;">\</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="shell"> <span class="nt" style="color: #000080;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$AUTHOR</span> <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="shell"></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="shell"><span class="nv" style="color: #008080;">progname</span><span class="o" style="font-weight: 600;">=</span>fps2sga.pl</span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="shell">help2man <span class="nt" style="color: #000080;">--no-info</span> <span class="nt" style="color: #000080;">--no-discard-stderr</span> <span class="nt" style="color: #000080;">--help-option</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">" -h"</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="shell"> <span class="nt" style="color: #000080;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"convert fps to sga"</span> <span class="se" style="color: #d14;">\</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="shell"> <span class="nt" style="color: #000080;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$AUTHOR</span> <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="shell"></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="shell"><span class="nv" style="color: #008080;">progname</span><span class="o" style="font-weight: 600;">=</span>gff2sga.pl</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="shell">help2man <span class="nt" style="color: #000080;">--no-info</span> <span class="nt" style="color: #000080;">--no-discard-stderr</span> <span class="nt" style="color: #000080;">--help-option</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">" -h"</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="shell"> <span class="nt" style="color: #000080;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"convert gff to sga"</span> <span class="se" style="color: #d14;">\</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="shell"> <span class="nt" style="color: #000080;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$AUTHOR</span> <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="shell"></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="shell"><span class="nv" style="color: #008080;">progname</span><span class="o" style="font-weight: 600;">=</span>partit2bed.pl</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="shell">help2man <span class="nt" style="color: #000080;">--no-info</span> <span class="nt" style="color: #000080;">--no-discard-stderr</span> <span class="nt" style="color: #000080;">--help-option</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">" -h"</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="shell"> <span class="nt" style="color: #000080;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"converts the output of the ChIP-Seq partitioning program to BED format"</span> <span class="se" style="color: #d14;">\</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="shell"> <span class="nt" style="color: #000080;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$AUTHOR</span> <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="shell"></span>
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<td class="diff-line-num new new_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="shell"><span class="nv" style="color: #008080;">progname</span><span class="o" style="font-weight: 600;">=</span>sga2bed</span>
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<td class="diff-line-num new new_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="shell">help2man <span class="nt" style="color: #000080;">--no-info</span> <span class="nt" style="color: #000080;">--no-discard-stderr</span> <span class="nt" style="color: #000080;">--help-option</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">" -h"</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="shell"> <span class="nt" style="color: #000080;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"Convert SGA format into BED format"</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="shell"> <span class="nt" style="color: #000080;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$AUTHOR</span> <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="shell"></span>
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<td class="diff-line-num new new_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="shell"><span class="nv" style="color: #008080;">progname</span><span class="o" style="font-weight: 600;">=</span>sga2fps.pl</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="shell">help2man <span class="nt" style="color: #000080;">--no-info</span> <span class="nt" style="color: #000080;">--no-discard-stderr</span> <span class="nt" style="color: #000080;">--help-option</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">" -h"</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="shell"> <span class="nt" style="color: #000080;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"Convert SGA format into FPS format"</span> <span class="se" style="color: #d14;">\</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="shell"> <span class="nt" style="color: #000080;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$AUTHOR</span> <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="shell"></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="shell"><span class="nv" style="color: #008080;">progname</span><span class="o" style="font-weight: 600;">=</span>sga2gff.pl</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="shell">help2man <span class="nt" style="color: #000080;">--no-info</span> <span class="nt" style="color: #000080;">--no-discard-stderr</span> <span class="nt" style="color: #000080;">--help-option</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">" -h"</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="shell"> <span class="nt" style="color: #000080;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"Convert SGA format into GFF format"</span> <span class="se" style="color: #d14;">\</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="shell"> <span class="nt" style="color: #000080;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$AUTHOR</span> <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="shell"><span class="nv" style="color: #008080;">progname</span><span class="o" style="font-weight: 600;">=</span>sga2wig</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="shell">help2man <span class="nt" style="color: #000080;">--no-info</span> <span class="nt" style="color: #000080;">--no-discard-stderr</span> <span class="nt" style="color: #000080;">--help-option</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">" -h"</span> <span class="se" style="color: #d14;">\</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="shell"> <span class="nt" style="color: #000080;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"Convert SGA format into Wiggle Track format"</span> <span class="se" style="color: #d14;">\</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="shell"> <span class="nt" style="color: #000080;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$AUTHOR</span> <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="shell"></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"*1.gz"</span> <span class="o" style="font-weight: 600;">></span> debian/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">PROGNAME</span><span class="k" style="font-weight: 600;">}</span>.manpages</span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$MANDIR</span><span class="s2" style="color: #d14;">/*.1"</span> <span class="o" style="font-weight: 600;">>></span> debian/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">PROGNAME</span><span class="k" style="font-weight: 600;">}</span>.manpages</span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="shell"></span>
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105
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<pre style="margin: 0;">+<span id="LC105" 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: #008080;">EOT</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="shell"><span class="sh" style="color: #d14;">Please enhance the help2man output.</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" 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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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="shell"><span class="sh" style="color: #d14;"> http://liw.fi/manpages/</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="shell"><span class="no" style="color: #008080;">EOT</span></span></pre>
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<a href="https://salsa.debian.org/med-team/chip-seq/-/compare/340f7777e3fe3f28dc5c46e996d0b6d63ccb2411...5c1c219674ea08aaf558f4c88a3a52e40719e5ce#68e0b13744e158347bfd74ebaaca667435f07d14"><strong>debian/manpages</strong>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">*1.gz</span></pre>
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<a href="https://salsa.debian.org/med-team/chip-seq/-/compare/340f7777e3fe3f28dc5c46e996d0b6d63ccb2411...5c1c219674ea08aaf558f4c88a3a52e40719e5ce#406d10df774ee8ef1b46900b89f07a8dabc751a9"><strong>debian/mans/bed2bed_display.1</strong></a>
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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 1.47.13.</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH BED2BED_DISPLAY "1" "March 2020" "bed2bed_display 1.5.5" "User Commands"</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">.SH NAME</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">bed2bed_display \- Convert BED file to BED format suitable for displaying ChIP-seq peaks.</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH SYNOPSIS</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">.B bed2bed_display</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">[\fI\,options\/\fR] [\fI\,-a <min BED score>\/\fR] [\fI\,-b <max BED score>\/\fR] [\fI\,<\/\fR] \fI\,<BED file|stdin>\/\fR</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">.SH DESCRIPTION</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">.IP</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">\- version 1.5.5</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">where options are:</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">.TP</span>
</pre>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">\fB\-d\fR|\-\-debug</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">Produce Debug information</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">.TP</span>
</pre>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">\fB\-h\fR|\-\-help</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">Show this Help text</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">.TP</span>
</pre>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">\fB\-f\fR|\-\-feature <ft></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">Set Feature name <ft></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">.TP</span>
</pre>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">\fB\-o\fR|\-\-oformat <1|2></span>
</pre>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">Set output Format (1:BED[Def] 2:BedGraph)</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">.TP</span>
</pre>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">\fB\-\-name\fR <name></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">Set name for track name field [def. name=SGA\-feature]</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">.TP</span>
</pre>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">\fB\-\-desc\fR <desc></span>
</pre>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">Set track description field [def. desc="ChIP\-Seq Custom data"]</span>
</pre>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">.TP</span>
</pre>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">\fB\-\-color\fR <col></span>
</pre>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">Define the track color in comma\-separated RGB values [def. 100,100,100]</span>
</pre>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">\fB\-\-autoscale\fR</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"><on|off> Data viewing paramenter: set auto\-scale to UCSC data view [def=OFF]</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">.TP</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">\fB\-\-always0\fR</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"><on|off> Data viewing paramenter: always include zero [def=OFF]</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">.TP</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">\fB\-\-wfunction\fR</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"><func> Data viewing paramenter: windowing function [def=mean+whiskers|maximum|mean|minimum]</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">\fB\-\-smoothing\fR</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"><grade> Data viewing paramenter: smoothing window [def=OFF[0], <grade>=0,2..16]</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">\fB\-\-visibility\fR <mode></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">Display mode: [def=dense|full|hide] or [def=1|2|3]</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">Convert BED file to BED format suitable for displaying ChIP\-seq peaks.</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">Two formats are supported: 1) BED Track with Score field; 2) BedGraph.</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">For BED track format, only the graphical parameter 'visibility' can be set.</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">.SH AUTHOR</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"> This manpage was written by Andreas Tille for the Debian distribution and</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext"> can be used for any other usage of the program.</span></pre>
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<li id="ba0e772a2b58bfe82d22bbbb80343c8740ebab9a">
<a href="https://salsa.debian.org/med-team/chip-seq/-/compare/340f7777e3fe3f28dc5c46e996d0b6d63ccb2411...5c1c219674ea08aaf558f4c88a3a52e40719e5ce#ba0e772a2b58bfe82d22bbbb80343c8740ebab9a"><strong>debian/mans/bed2sga.1</strong></a>
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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 1.47.13.</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH BED2SGA "1" "March 2020" "bed2sga 1.5.5" "User Commands"</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">bed2sga \- Convert BED format into SGA format.</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH SYNOPSIS</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">.B bed2sga</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">[\fI\,options\/\fR] [\fI\,-s <s_assembly (e.g. hg19)>\/\fR] [\fI\,<\/\fR] \fI\,<BED file|stdin>\/\fR</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">.SH DESCRIPTION</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">.IP</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">\- version 1.5.5</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">where options are:</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">.TP</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">\fB\-d\fR|\-\-debug</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">Produce Debug information</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">.TP</span>
</pre>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">\fB\-h\fR|\-\-help</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">Show this Help text</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">\fB\-i\fR|\-\-db <path></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">Use <path> to locate the assembly\-specific chr_NC_gi file</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">[default is: $HOME/db/genome]</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">.TP</span>
</pre>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">\fB\-f\fR|\-\-feature <ft></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">Set Feature name <ft></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">.TP</span>
</pre>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">\fB\-s\fR|\-\-species <spec></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">Assembly <spec> (i.e hg19)</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">.TP</span>
</pre>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">\fB\-c\fR|\-\-center</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">Generate a Centered SGA file</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">.TP</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">\fB\-u\fR|\-\-unoriented</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">Generate an unoriented SGA file</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">\fB\-r\fR|\-\-regional</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">Generate a 2\-line[+/\-] SGA file representing BED regions</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">(e.g. RepeatMasker regions)</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">.TP</span>
</pre>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">\fB\-e\fR|\-\-extend <f1,f2,...></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">Produce an extended SGA file with additional fields specified</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">by a comma\-separated list of BED column numbers (from 1 to n)</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">.TP</span>
</pre>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">\fB\-\-useScore\fR</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">Use the BED 'score' field (#5) to set the SGA 'count' field</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">.TP</span>
</pre>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">\fB\-\-useSigVal\fR</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">Use the BED 'Signal Value' field (#7) to set the SGA 'count' field</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">[This option is only valid for ENCODE narrowPeak]</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">.TP</span>
</pre>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">\fB\-\-narrowPeak\fR</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">Use this option for ENCODE narrowPeak format</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">[Options \fB\-\-useScore\fR, \fB\-c\fR, and \fB\-u\fR are ignored]</span>
</pre>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">.IP</span>
</pre>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">Convert BED format into SGA format.</span>
</pre>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">.SH AUTHOR</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext"> This manpage was written by Andreas Tille for the Debian distribution and</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext"> can be used for any other usage of the program.</span></pre>
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<li id="37296ab03814e440a642152108e8e3be70fdd549">
<a href="https://salsa.debian.org/med-team/chip-seq/-/compare/340f7777e3fe3f28dc5c46e996d0b6d63ccb2411...5c1c219674ea08aaf558f4c88a3a52e40719e5ce#37296ab03814e440a642152108e8e3be70fdd549"><strong>debian/mans/compactsga.1</strong></a>
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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 1.47.13.</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH COMPACTSGA "1" "March 2020" "compactsga 1.5.5" "User Commands"</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">compactsga \- reads a ChIP-seq data file and merges equal tag positions into a single line</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH SYNOPSIS</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">.B compactsga</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">[\fI\,options\/\fR] \fI\,< <SGA File>\/\fR</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">.SH DESCRIPTION</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">\- version 1.5.5</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">where options are:</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">\fB\-h\fR</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">Show this help text</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">\fB\-d\fR</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">Print debug information</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">The program reads a ChIP\-seq data file in SGA format (<SGA File>),</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">and merges equal tag positions into a single line adjusting the count</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">field accordingly</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">.SH AUTHOR</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> This manpage was written by Andreas Tille for the Debian distribution and</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> can be used for any other usage of the program.</span></pre>
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<li id="27f4fb020354d6d3056ff8281ab8e61c7c7a87cd">
<a href="https://salsa.debian.org/med-team/chip-seq/-/compare/340f7777e3fe3f28dc5c46e996d0b6d63ccb2411...5c1c219674ea08aaf558f4c88a3a52e40719e5ce#27f4fb020354d6d3056ff8281ab8e61c7c7a87cd"><strong>debian/mans/countsga.1</strong></a>
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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 1.47.13.</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH COUNTSGA "1" "March 2020" "countsga 1.5.5" "User Commands"</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">countsga \- read a ChIP-seq data file and computes the total number of tag counts</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH SYNOPSIS</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">.B countsga</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">[\fI\,options\/\fR] [\fI\,<\/\fR] \fI\,<SGA File>\/\fR</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">.SH DESCRIPTION</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">.IP</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">\- version 1.5.5</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">where options are:</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">.TP</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">\fB\-h\fR</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">Show this help text</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">.TP</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">\fB\-d\fR</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">Print debug information</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">.TP</span>
</pre>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">\fB\-f\fR</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">Feature specifications [name [+|\-]]</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">\fB\-c\fR</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">Count Cut\-off (default is 1)</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">The program reads a ChIP\-seq data file (or from stdin [<]) in SGA format (<SGA File>),</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">and computes the total number of tag counts as well as the total sequence length.</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">The <Feature> parameter is a name that corresponds to the second field of the SGA file.</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">It might optionally include the strand specification (+|\-).</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">If no feature is given then all input tags are processed.</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">.SH AUTHOR</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> This manpage was written by Andreas Tille for the Debian distribution and</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> can be used for any other usage of the program.</span></pre>
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<li id="4e4a2cf6f450babce42b27ec34be504e9d4de33a">
<a href="https://salsa.debian.org/med-team/chip-seq/-/compare/340f7777e3fe3f28dc5c46e996d0b6d63ccb2411...5c1c219674ea08aaf558f4c88a3a52e40719e5ce#4e4a2cf6f450babce42b27ec34be504e9d4de33a"><strong>debian/mans/featreplace.1</strong></a>
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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 1.47.13.</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH FEATREPLACE "1" "March 2020" "featreplace 1.5.5" "User Commands"</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">featreplace \- read a ChIP-seq data file and changes the name of the feature field</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH SYNOPSIS</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">.B featreplace</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">[\fI\,options\/\fR] \fI\,-f <feature name> \/\fR[\fI\,<\/\fR] \fI\,<SGA File>\/\fR</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">.SH DESCRIPTION</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">\- version 1.5.5</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">where options are:</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">\fB\-h\fR</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">Show this help text</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">\fB\-d\fR</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">Print debug information</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">The program reads a ChIP\-seq data file (or from stdin [<]) in SGA format (<SGA File>),</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">and changes the name of the feature field according to the specified parameter <feature name></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">(by default <feature name>='FT').</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">.SH AUTHOR</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> This manpage was written by Andreas Tille for the Debian distribution and</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> can be used for any other usage of the program.</span></pre>
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<li id="e52ff9008ba9438986bc2b3c47e61a6e0eef5bcc">
<a href="https://salsa.debian.org/med-team/chip-seq/-/compare/340f7777e3fe3f28dc5c46e996d0b6d63ccb2411...5c1c219674ea08aaf558f4c88a3a52e40719e5ce#e52ff9008ba9438986bc2b3c47e61a6e0eef5bcc"><strong>debian/mans/filter_counts.1</strong></a>
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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 1.47.13.</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH FILTER_COUNTS "1" "March 2020" "filter_counts 1.5.5" "User Commands"</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">filter_counts \- read a ChIP-seq data file and filters out all read counts</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH SYNOPSIS</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">.B filter_counts</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">[\fI\,options\/\fR] [\fI\,<\/\fR] \fI\,<SGA File>\/\fR</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">.SH DESCRIPTION</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">\- version 1.5.5</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">where options are:</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">\fB\-h\fR</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">Show this help text</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">\fB\-d\fR</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">Print debug information</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">\fB\-f\fR</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">Feature defining the user\-defined regions of interest (default=RMSK)</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">.TP</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">\fB\-r\fR</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">Retain Mode on</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">.IP</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">The program reads a ChIP\-seq data file (or from stdin [<]) in SGA format (<SGA File>)</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">and filters out all read counts that occur within user\-defined regions of interest, such</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">as Repeat Mask regions (feature=RMSK).</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">If 'Retain Mode' is on, it only retains those lines that are within the user\-defined regions,</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">in which case the annotation of the user\-defined regions is added to the output SGA file.</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">.SH AUTHOR</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> This manpage was written by Andreas Tille for the Debian distribution and</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> can be used for any other usage of the program.</span></pre>
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<li id="e86578b0d1dbef8f60921d329b45f6d79bc3345b">
<a href="https://salsa.debian.org/med-team/chip-seq/-/compare/340f7777e3fe3f28dc5c46e996d0b6d63ccb2411...5c1c219674ea08aaf558f4c88a3a52e40719e5ce#e86578b0d1dbef8f60921d329b45f6d79bc3345b"><strong>debian/mans/fps2sga.pl.1</strong></a>
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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 1.47.13.</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH FPS2SGA.PL "1" "March 2020" "fps2sga.pl 1.5.5" "User Commands"</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">fps2sga.pl \- convert fps to sga</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH DESCRIPTION</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">fps2sga.pl [options] <FPS file></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">where options are:</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">\fB\-h\fR|\-\-help</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Show this stuff</span>
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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">.TP</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">\fB\-f\fR|\-\-feature <feature></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">Set Feature name <feature></span>
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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">\fB\-s\fR|\-\-species <species></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">Assembly <species> (i.e hg18)</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">
19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">.TP</span>
</pre>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">\fB\-x\fR</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">Generate an extended SGA file with the</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">6th field equal to the FPS 'description' field</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">.TP</span>
</pre>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">\fB\-\-ignore0flag\fR</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">Ignore 0 flag at position 29 of the FP line,</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">so keep orientation the same as original</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">.SH AUTHOR</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> This manpage was written by Andreas Tille for the Debian distribution and</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> can be used for any other usage of the program.</span></pre>
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<li id="96ff0c1a27b68a94a0bc4e272c2df80c2e26a6f4">
<a href="https://salsa.debian.org/med-team/chip-seq/-/compare/340f7777e3fe3f28dc5c46e996d0b6d63ccb2411...5c1c219674ea08aaf558f4c88a3a52e40719e5ce#96ff0c1a27b68a94a0bc4e272c2df80c2e26a6f4"><strong>debian/mans/gff2sga.pl.1</strong></a>
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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 1.47.13.</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH GFF2SGA.PL "1" "March 2020" "gff2sga.pl 1.5.5" "User Commands"</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">.SH NAME</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">gff2sga.pl \- convert gff to sga</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH DESCRIPTION</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">.IP</span>
</pre>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">gff2sga.pl [options] <GFF file></span>
</pre>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">.IP</span>
</pre>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">where options are:</span>
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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">.TP</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">
11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">\fB\-h\fR|\-\-help</span>
</pre>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Show this stuff</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">
13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">\fB\-\-db\fR <path></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">Use <path> to locate Chrom Id Storable File 'chro_idx.nstorage'</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">
16
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<pre style="margin: 0;">+<span id="LC16" 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="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">\fB\-f\fR|\-\-feature <feature></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">
18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">Set Feature name <feature></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="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="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">\fB\-s\fR|\-\-species <species></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">Assembly <species> (i.e hg18)</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">.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="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">\fB\-c\fR</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="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">Generate a Centered SGA 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="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
25
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<pre style="margin: 0;">+<span id="LC25" 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="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">\fB\-u\fR</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="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">Generate an Unoriented SGA file</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
28
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<pre style="margin: 0;">+<span id="LC28" 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="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">\fB\-x\fR</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="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">Generate an extended SGA file with the</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">6th field equal to the GFF 'feature' field,</span>
</pre>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">and the feature field equal to the GFF 'source'</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">.SH AUTHOR</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> This manpage was written by Andreas Tille for the Debian distribution and</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> can be used for any other usage of the program.</span></pre>
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<li id="b9a4899642c1c76fbabf5d82080be8de13d0b016">
<a href="https://salsa.debian.org/med-team/chip-seq/-/compare/340f7777e3fe3f28dc5c46e996d0b6d63ccb2411...5c1c219674ea08aaf558f4c88a3a52e40719e5ce#b9a4899642c1c76fbabf5d82080be8de13d0b016"><strong>debian/mans/partit2bed.pl.1</strong></a>
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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 1.47.13.</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH PARTIT2BED.PL "1" "March 2020" "partit2bed.pl 1.5.5" "User Commands"</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">partit2bed.pl \- converts the output of the ChIP-Seq partitioning program to BED format</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH DESCRIPTION</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">partit2bed.pl [options] <ChIP\-Part out file></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">where options are:</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">\fB\-h\fR|\-\-help</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Show this stuff</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">\fB\-\-db\fR <path></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">Use <path> to locate Chrom Id Storable File 'chro_idx.nstorage'</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">\fB\-t\fR|\-\-track <track></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">BED track name [def: Test\-BED]</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">\fB\-d\fR|\-\-desc <desc></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">Description field of the BED header line [def: ChIP\-Seq]</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">.TP</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">\fB\-n\fR <int></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">Chromosome number (BED declaration lines) [def: 0 \- all chromosomes]</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">.TP</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">\fB\-b\fR <int></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">Chromosome start [def: \fB\-1\fR \- entire chrom region]</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">.TP</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">\fB\-e\fR <int></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">Chromosome end [def: \fB\-1\fR \- entire chrom region]</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">The program converts the output of the ChIP\-Seq partitioning program to BED format.</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">.SH AUTHOR</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> This manpage was written by Andreas Tille for the Debian distribution and</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> can be used for any other usage of the program.</span></pre>
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</li>
<li id="58d99a432a997aa43330a4bdeb9e028feb358a4a">
<a href="https://salsa.debian.org/med-team/chip-seq/-/compare/340f7777e3fe3f28dc5c46e996d0b6d63ccb2411...5c1c219674ea08aaf558f4c88a3a52e40719e5ce#58d99a432a997aa43330a4bdeb9e028feb358a4a"><strong>debian/mans/sga2bed.1</strong></a>
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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 1.47.13.</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH SGA2BED "1" "March 2020" "sga2bed 1.5.5" "User Commands"</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">sga2bed \- Convert SGA format into BED format</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH SYNOPSIS</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">.B sga2bed</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">[\fI\,options\/\fR] [\fI\,<\/\fR] \fI\,<SGA file|stdin>\/\fR</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">.SH DESCRIPTION</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">\- version 1.5.5</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">where options are:</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">.TP</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">\fB\-d\fR|\-\-debug</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">Produce Debug information</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">.TP</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">\fB\-h\fR|\-\-help</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">Show this Help text</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">.TP</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">\fB\-i\fR|\-\-db <path></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">Use <path> to locate the chr_NC_gi file</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">[default is: $HOME/db/genome]</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">.TP</span>
</pre>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">\fB\-l\fR|\-\-readlen <len></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">Set Read length <len></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">Unoriented SGA files are extended by +/\-<len>/2</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">.TP</span>
</pre>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">\fB\-c\fR|\-\-score <score></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">Normalisation factor for BED score field (5th) [score=1]</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">.TP</span>
</pre>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">\fB\-n\fR|\-\-norm</span>
</pre>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"><normf> Normalisation factor for BED score field (7th) [normf=1]</span>
</pre>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">.TP</span>
</pre>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">\fB\-e\fR|\-\-extend f1:F1[,f2:F2] Set SGA optional field(s) f1(,f2,...) to BED field(s) F1,(F2,..)</span>
</pre>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">Fields are specified by column numbers</span>
</pre>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">Accepted BED field values are 4, 5, and 7</span>
</pre>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">Except BED field 5 (score field), BED fields 4 and 7</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">can be used to set multiple extension values from SGA</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">Fields 5 and 7 convert into numerical values whereas</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">BED field 4 takes character strings as they are</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">.TP</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">\fB\-r\fR|\-\-nohdr</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">BED format without annotation track header lines</span>
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<td class="diff-line-num new new_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">.TP</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">\fB\-x\fR|\-\-expand</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">Expand SGA lines into multiple BED lines</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">.TP</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">\fB\-\-name\fR <name></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">Set name for track name field [def. name=SGA\-feature]</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">\fB\-\-desc\fR <desc></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">Set track description field [def. desc="ChIP\-Seq Custom data"]</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">\fB\-\-color\fR <col></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">Define the track color in comma\-separated RGB values [def. 100,100,100]</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">Convert SGA format into BED format.</span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">.SH AUTHOR</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext"> This manpage was written by Andreas Tille for the Debian distribution and</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext"> can be used for any other usage of the program.</span></pre>
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<li id="f56abfaa2778699e2bfc82e6d68c1ac1678f1048">
<a href="https://salsa.debian.org/med-team/chip-seq/-/compare/340f7777e3fe3f28dc5c46e996d0b6d63ccb2411...5c1c219674ea08aaf558f4c88a3a52e40719e5ce#f56abfaa2778699e2bfc82e6d68c1ac1678f1048"><strong>debian/mans/sga2fps.pl.1</strong></a>
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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 1.47.13.</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH SGA2FPS.PL "1" "March 2020" "sga2fps.pl 1.5.5" "User Commands"</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">.SH NAME</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">sga2fps.pl \- Convert SGA format into FPS format</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH DESCRIPTION</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">.IP</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">sga2fps.pl [options] <SGA file|stdin></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">.IP</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">
9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">where options are:</span>
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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">.TP</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">
11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">\fB\-h\fR|\-\-help</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Show this stuff</span>
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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">.TP</span>
</pre>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">\fB\-\-db\fR <path></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">Use <path> to locate Chrom Id Storable File 'chro_idx.nstorage'</span>
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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">.TP</span>
</pre>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">\fB\-f\fR <feature></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">Set <feature> field</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">
19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">\fB\-s\fR|\-\-species <species></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">Assembly <species> (i.e hg18)</span>
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<td class="diff-line-num new new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">\fB\-\-set0flag\fR</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">Set 0 flag at postion 29 of the FP line, forcing unoriented output</span>
</pre>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">(default : blank)</span>
</pre>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">.SH AUTHOR</span>
</pre>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> This manpage was written by Andreas Tille for the Debian distribution and</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> can be used for any other usage of the program.</span></pre>
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<li id="0c6939d517692a3ad80e2549605b22c77851e168">
<a href="https://salsa.debian.org/med-team/chip-seq/-/compare/340f7777e3fe3f28dc5c46e996d0b6d63ccb2411...5c1c219674ea08aaf558f4c88a3a52e40719e5ce#0c6939d517692a3ad80e2549605b22c77851e168"><strong>debian/mans/sga2gff.pl.1</strong></a>
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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 1.47.13.</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH SGA2GFF.PL "1" "March 2020" "sga2gff.pl 1.5.5" "User Commands"</span>
</pre>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">.SH NAME</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">sga2gff.pl \- Convert SGA format into GFF format</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH DESCRIPTION</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">.IP</span>
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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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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">sga2gff.pl [options] <SGA file></span>
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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">.IP</span>
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">where options are:</span>
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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">.TP</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">
11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">\fB\-h\fR|\-\-help</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Show this stuff</span>
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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">\fB\-\-db\fR <path></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">
15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">Use <path> to locate Chrom Id Storable File 'chro_idx.nstorage'</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">
16
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<pre style="margin: 0;">+<span id="LC16" 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="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">\fB\-l\fR|\-\-taglen <taglen></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">
18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">Set Read length <taglen></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="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="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">\fB\-x\fR</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="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">Expand SGA lines into multiple GFF lines</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="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">.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="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">\fB\-e\fR|\-\-ext <ext_flag></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="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">Use SGA 6th field to set GFF feature field</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">
</td>
<td class="diff-line-num new new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">and store SGA feature into GFF source field</span>
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<td class="diff-line-num new new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">.SH AUTHOR</span>
</pre>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> This manpage was written by Andreas Tille for the Debian distribution and</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> can be used for any other usage of the program.</span></pre>
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<li id="306ad0e42c6d098ddeb6d6d7db32c47f84689c7f">
<a href="https://salsa.debian.org/med-team/chip-seq/-/compare/340f7777e3fe3f28dc5c46e996d0b6d63ccb2411...5c1c219674ea08aaf558f4c88a3a52e40719e5ce#306ad0e42c6d098ddeb6d6d7db32c47f84689c7f"><strong>debian/mans/sga2wig.1</strong></a>
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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 1.47.13.</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH SGA2WIG "1" "March 2020" "sga2wig 1.5.5" "User Commands"</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">sga2wig \- Convert SGA format into Wiggle Track format</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH SYNOPSIS</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">.B sga2wig</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">[\fI\,options\/\fR] [\fI\,<\/\fR] \fI\,<SGA file|stdin>\/\fR</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">.SH DESCRIPTION</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">\- version 1.5.5</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">where options are:</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">\fB\-d\fR|\-\-debug</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">Produce Debug information</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">\fB\-h\fR|\-\-help</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">Show this Help text</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">\fB\-i\fR|\-\-db <path></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">Use <path> to locate the chr_NC_gi and chr_size files</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">[default is: $HOME/db/genome]</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">\fB\-o\fR|\-\-format <0|1></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">Set Wiggle Track data format: variableStep[def=0]/fixedStep[1]</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">.TP</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">\fB\-n\fR|\-\-chrnb</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"><int> Chromosome number [def: 0 (all chromosomes)]</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">.TP</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">\fB\-b\fR|\-\-start</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"><int> Chromosome start [def: \fB\-1\fR (entire chromosome)]</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">.TP</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">\fB\-e\fR|\-\-end</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"><int> Chromosome end [def: \fB\-1\fR (entire chromosome)]</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">\fB\-c\fR|\-\-coff</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"><int> Count cut\-off for the SGA input file [def=99999]</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">.TP</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">\fB\-s\fR|\-\-span</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"><int> Wiggle Track Span(\fI\,/stepInterval\/\fP) parameter [def=150]</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">.IP</span>
</pre>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">For fixedStep data format, it defines the step parameter</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">.TP</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">\fB\-f\fR|\-\-norm</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"><int> Normalization factor for total tag counts within step intervals [def=0]</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">.IP</span>
</pre>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">This option is only valid for fixedStep data format</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">.TP</span>
</pre>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">\fB\-\-peakf\fR</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">Indicate that the The SGA input file represents a peak file</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">[i.e. coordinates are peak centers]</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">In such case, the span range begins upstream of [span=]150 bp</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">chromosome position specified, and ends [span=]150 bp downstream</span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">.TP</span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">\fB\-\-name\fR <name></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">Set name for track name field [def. name=SGA\-feature]</span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">.TP</span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">\fB\-\-desc\fR <desc></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">Set track description field [def. desc="ChIP\-Seq Custom data"]</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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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">\fB\-\-color\fR <col></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">Define the track color in comma\-separated RGB values [def. 100,100,100]</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">\fB\-\-autoscale\fR</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext"><on|off> Data viewing paramenter: set auto\-scale to UCSC data view [def=OFF]</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">.TP</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">\fB\-\-always0\fR</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext"><on|off> Data viewing paramenter: always include zero [def=OFF]</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">.TP</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext">\fB\-\-wfunction\fR</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext"><func> Data viewing paramenter: windowing function [def=mean+whiskers|maximum|mean|minimum]</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext">.TP</span>
</pre>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext">\fB\-\-smoothing\fR</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext"><grade> Data viewing paramenter: smoothing window [def=OFF[0], <grade>=0,2..16]</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">\fB\-\-visibility\fR <mode></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext">Display mode: [def=full|dense|hide]</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext">.IP</span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext">Convert SGA format into Wiggle Track format (WIG).</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext">WIG format is line\-oriented, and is composed of declaration lines and data lines.</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext">.IP</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext">\- variableStep is for data with irregular intervals between new data points.</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext">.IP</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext">It begins with a declaration line and is followed by two columns containing chromosome positions and data values:</span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext">.TP</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext">variableStep</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext">chrom=chrN [span=windowSize]</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">chromStartA</span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext">dataValueA</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext">.TP</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext">chromStartB</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext">dataValueB</span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext">.TP</span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext">\&... etc ...</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext">\&... etc ...</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext">.IP</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext">\- fixedStep is for data with regular intervals between new data values.</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext">.IP</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext">It begins with a declaration line and is followed by a single column of data values:</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext">.TP</span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext">fixedStep</span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext">chrom=chrN start=position step=stepInterval [span=windowSize = stepInterval]</span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext">dataValue1</span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext">dataValue2</span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext">\&... etc ...</span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext">.SH AUTHOR</span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext"> This manpage was written by Andreas Tille for the Debian distribution and</span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext"> can be used for any other usage of the program.</span></pre>
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<li id="91629de237e1cfa7686ea02d3c8ee710c369ec8b">
<a href="https://salsa.debian.org/med-team/chip-seq/-/compare/340f7777e3fe3f28dc5c46e996d0b6d63ccb2411...5c1c219674ea08aaf558f4c88a3a52e40719e5ce#91629de237e1cfa7686ea02d3c8ee710c369ec8b"><strong>debian/patches/data_location.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Mon, 23 Mar 2020 20:55:38 +0100</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Description: Adapt database installation PATH to Debian location</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">--- a/tools/chr_replace_sga.pl</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tools/chr_replace_sga.pl</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -9,7 +9,7 @@</span> use Storable qw (retrieve nstore);</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> my %opts;</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> getopt('sf:', \%opts); # -s, & -f take arg. Values in %opts, Hash keys will be the switch names</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-my $DB = "/db/genome/";</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+my $DB = "/usr/share/chip-seq/";</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> #my $DB = "/home/local/db/genome/";</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> my $chr2SV = retrieve($DB."chro_idx.nstorage");</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tools/sga2fps.pl</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tools/sga2fps.pl</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="p">@@ -19,7 +19,7 @@</span> my $feature = "";</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> my $ft_flag = 0;</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> my $set0flag = 0;</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> #my $DB = "/home/local/db/genome/";</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-my $DB = "/db/genome/";</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+my $DB = "/usr/share/chip-seq/";</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> if( ! GetOptions( \%opt, @options ) ) { &Usage(); }</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tools/sga2gff.pl</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tools/sga2gff.pl</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="p">@@ -17,7 +17,7 @@</span> my $taglen = 0;</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> my $expand = 0;</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> my $ext_flag = 0;</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> #my $DB = "/home/local/db/genome/";</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-my $DB = "/db/genome/";</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+my $DB = "/usr/share/chip-seq/";</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> if( ! GetOptions( \%opt, @options ) ) { &Usage(); }</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tools/check_bed.pl</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tools/check_bed.pl</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="p">@@ -9,7 +9,7 @@</span> use Storable qw (retrieve nstore);</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> my %opts;</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> getopt('sf:', \%opts); # -s, & -f take arg. Values in %opts, Hash keys will be the switch names</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-my $DB = "/db/genome/";</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+my $DB = "/usr/share/chip-seq/";</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> #my $DB = "/home/local/db/genome/";</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> my $chr2SV = retrieve($DB."chro_idx.nstorage");</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tools/eland2sga.pl</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tools/eland2sga.pl</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="p">@@ -13,7 +13,7 @@</span> getopt('asf:', \%opts); # -a, -s, & -f</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> die("\nusage: eland2sga.pl -a feature -s species -f eland_file\n\n") unless (($opts{'f'})&&($opts{'a'})&&($opts{'s'}));</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> # hash defining chromosome from SV of chromosomes in current genome assemblies</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-my $DB = "/db/genome/";</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+my $DB = "/usr/share/chip-seq/";</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> #my $DB = "/home/local/db/genome/";</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> my $chr2AC = retrieve($DB."chro_idx.nstorage");</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> # eventually add older assemblies?</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tools/gff2sga.pl</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tools/gff2sga.pl</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="p">@@ -25,7 +25,7 @@</span> my $ext_sc = 0;</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> my $score = 0;</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"> #my $DB = "/home/local/db/genome/";</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-my $DB = "/db/genome/";</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+my $DB = "/usr/share/chip-seq/";</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"> </span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"> if( ! GetOptions( \%opt, @options ) ) { &Usage(); }</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> </span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tools/partit2bed.pl</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tools/partit2bed.pl</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="p">@@ -17,7 +17,7 @@</span> my $chr_nb = "chr0";</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"> my $chr_start = -1;</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"> my $chr_end = -1;</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"> #my $DB = "/home/local/db/genome/";</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-my $DB = "/db/genome/";</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+my $DB = "/usr/share/chip-seq/";</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"> </span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"> if( ! GetOptions( \%opt, @options ) ) { &Usage(); }</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"> &Usage() if defined($opt{'help'}) || defined($opt{'h'});</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tools/partit2gff.pl</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tools/partit2gff.pl</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"><span class="p">@@ -10,7 +10,7 @@</span> use strict;</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"> use Storable qw (retrieve nstore); # package to store persistently variables in files [http://search.cpan.org/author/AMS/Storable-2.07/Storable.pm]</span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"> # hash defining chromosome from SV of chromosomes in current genome assemblies</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-my $chr2SV = retrieve("/db/genome/chro_idx.nstorage");</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+my $chr2SV = retrieve("/usr/share/chip-seq/chro_idx.nstorage");</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"> </span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"> my @pos = ();</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"> my $count = 0;</span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tools/partit2sga.pl</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tools/partit2sga.pl</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"><span class="p">@@ -10,7 +10,7 @@</span> use Storable qw (retrieve nstore);</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"> my %opt;</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"> my @options = ("help", "h", "db=s");</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"> </span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-my $DB = "/home/local/db/genome/";</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+my $DB = "/usr/share/chip-seq/";</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"> #my $DB = "/db/genome/";</span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"> </span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"> if( ! GetOptions( \%opt, @options ) ) { &Usage(); }</span></pre>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/chip-seq/-/compare/340f7777e3fe3f28dc5c46e996d0b6d63ccb2411...5c1c219674ea08aaf558f4c88a3a52e40719e5ce#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">fix_makefile.patch</span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"># fix_install.patch</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">data_location.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/chip-seq/-/compare/340f7777e3fe3f28dc5c46e996d0b6d63ccb2411...5c1c219674ea08aaf558f4c88a3a52e40719e5ce#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">@@ -2,6 +2,8 @@</td>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"># DH_VERBOSE := 1</span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">include /usr/share/dpkg/default.mk</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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5
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">%:</span>
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6
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> dh $@</span>
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -10,3 +12,10 @@ override_dh_install:</td>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> for perlscript in `grep -lR '#!/usr/local/bin/perl' debian/*/usr` ; do \</span>
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11
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<td class="diff-line-num new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> sed -i '1s+#!/usr/local/bin/perl+#!/usr/bin/perl+' $${perlscript} ; \</span>
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<td class="diff-line-num old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
12
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<td class="diff-line-num new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> done</span>
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<td class="diff-line-num new old_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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<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">
15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"></span>
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<td class="diff-line-num new old_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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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">override_dh_installman:</span>
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<td class="diff-line-num new old_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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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> dh_installman --language=C</span>
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<td class="diff-line-num new old_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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<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">
18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"></span>
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<td class="diff-line-num new old_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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<td class="diff-line-num new new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">override_dh_fixperms:</span>
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<td class="diff-line-num new old_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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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> dh_fixperms</span>
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<td class="diff-line-num new old_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="LC21" class="line" lang="plaintext"> find debian/$(DEB_SOURCE)-data/usr/share/$(DEB_SOURCE)/ -type f -exec chmod -x \{\} \;</span></pre>
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