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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/htseq">Debian Med / htseq</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/htseq/commit/4dc606ecd11140eb01a552c16d7cc891b1d29c8f">4dc606ec</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-05-01T11:18:52+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Binaries are provided in python3-htseq package
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/htseq/commit/aa30f62112bfe969f75bbdf414b2715687ab4fa7">aa30f621</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-05-01T11:23:17+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">hardening=+all
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/htseq/commit/0210410739af4d439f15b4a15edbf402bc7d9e05">02104107</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-05-01T11:25:41+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Provide manpages from old version (FIXME: Needs verification whether it is correct for new version)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/htseq/commit/bdbd3b76726c6efbaf85be5f02d068747d06fa82">bdbd3b76</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-05-01T11:29:37+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Secure URI in watch file (pointing to new PyPi)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/htseq/commit/eb09d4b9ab88068180ac7aefd3fd96bbdabdc8ca">eb09d4b9</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-05-01T11:35:50+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix spelling
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/htseq/commit/ca6807052dce671b9c96149b9c0468f9826ef5b4">ca680705</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-05-01T11:36:25+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Testsuite: autopkgtest-pkg-python
</pre>
</li>
</ul>
<h4>7 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#36e006c3a6b2ee635a212d5c06b612d0f2a3ea52">
<span class="new-file">
+
debian/man/htseq-count.1
</span>
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</li>
<li class="file-stats">
<a href="#a18e68093b9966efb5679aea8d79db88105c7396">
<span class="new-file">
+
debian/man/htseq-qa.1
</span>
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<li class="file-stats">
<a href="#f5bb5c2f86e675f64484fae13f789f4c43d473aa">
<span class="new-file">
+
debian/python3-htseq.manpages
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
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<li class="file-stats">
<a href="#68ef9f98c01c7eecd4c605cc26048a06f3304b79">
debian/watch
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/htseq/compare/1a15a0f9fdf71bda8cfc3359ccba32da18a556af...ca6807052dce671b9c96149b9c0468f9826ef5b4#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">htseq (0.9.1-1) <span class="idiff left right">UNRELEASED</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">htseq (0.9.1-1) <span class="idiff left right">unstable</span>; urgency=medium</span>
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<td class="diff-line-num new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> * New upstream version</span>
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<td class="diff-line-num old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * Point Vcs fields to salsa.debian.org</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8,8 +8,13 @@ htseq (0.9.1-1) UNRELEASED; urgency=medium</td>
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<td class="diff-line-num old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> - Remove unused get-orig-source target</span>
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<td class="diff-line-num old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> - There is no clean script any more so remove the specific targets</span>
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<td class="diff-line-num old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> * Sphinx doc does not seem to reported any more</span>
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<td class="diff-line-num new old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> * Provide Python3 package</span>
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<td class="diff-line-num new old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> * Binaries are provided in python3-htseq package</span>
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<td class="diff-line-num new old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> * hardening=+all</span>
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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> * Secure URI in watch file (pointing to new PyPi)</span>
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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> * Testsuite: autopkgtest-pkg-python</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Tue, 01 May 2018 <span class="idiff left right">07:49:00</span> +0200</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Tue, 01 May 2018 <span class="idiff left right">11:29:55</span> +0200</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">htseq (0.6.1p1-4) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/htseq/compare/1a15a0f9fdf71bda8cfc3359ccba32da18a556af...ca6807052dce671b9c96149b9c0468f9826ef5b4#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,6 +3,7 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Uploaders: Diane Trout <diane@ghic.org>,</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Section: python</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Testsuite: autopkgtest-pkg-python</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">Build-Depends: debhelper (>= 11~),</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> python-debian,</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">@@ -52,7 +53,7 @@ Depends: ${misc:Depends},</td>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="plaintext"> ${python3:Depends},</span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="plaintext"> ${shlibs:Depends}</span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="plaintext">Breaks: python-htseq (<= 0.9.1)</span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="plaintext">Provides: python-htseq<span class="idiff left right"> (<= 0.9.1)</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">Provides: python-htseq</span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="plaintext">Description: Python3 high-throughput genome sequencing read analysis utilities</span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="plaintext"> HTSeq can be used to performing a number of common analysis tasks</span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="plaintext"> when working with high-throughput genome sequencing reads:</span>
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<a href="https://salsa.debian.org/med-team/htseq/compare/1a15a0f9fdf71bda8cfc3359ccba32da18a556af...ca6807052dce671b9c96149b9c0468f9826ef5b4#36e006c3a6b2ee635a212d5c06b612d0f2a3ea52"><strong>debian/man/htseq-count.1</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.\" Man page generated from reStructuredText.</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">.TH "HTSEQ-COUNT" "1" "Oct 01, 2017" "0.6.1p1" "HTSeq"</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">htseq-count \- Count the number of reads in a SAM alignment file that map to GFF features</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">.</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">.nr rst2man-indent-level 0</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">.</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">.de1 rstReportMargin</span>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="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">\\$1 \\n[an-margin]</span>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="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">level \\n[rst2man-indent-level]</span>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">level margin: \\n[rst2man-indent\\n[rst2man-indent-level]]</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="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
13
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">-</span>
</pre>
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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="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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">\\n[rst2man-indent0]</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="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
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">\\n[rst2man-indent1]</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="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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">\\n[rst2man-indent2]</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">..</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="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">.de1 INDENT</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="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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">.\" .rstReportMargin pre:</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">. RS \\$1</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="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">. nr rst2man-indent\\n[rst2man-indent-level] \\n[an-margin]</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">. nr rst2man-indent-level +1</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">.\" .rstReportMargin post:</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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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">..</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">.de UNINDENT</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">. RE</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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">.\" indent \\n[an-margin]</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="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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">.\" old: \\n[rst2man-indent\\n[rst2man-indent-level]]</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">.nr rst2man-indent-level -1</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">.\" new: \\n[rst2man-indent\\n[rst2man-indent-level]]</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="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">.in \\n[rst2man-indent\\n[rst2man-indent-level]]u</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="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">..</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">.sp</span>
</pre>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">Given a file with aligned sequencing reads and a list of genomic</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">features, a common task is to count how many reads map to each feature.</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">.sp</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">A feature is here an interval (i.e., a range of positions) on a chromosome</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">or a union of such intervals.</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">.sp</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">In the case of RNA\-Seq, the features are typically genes, where each gene</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">is considered here as the union of all its exons. One may also consider</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">each exon as a feature, e.g., in order to check for alternative splicing.</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">For comparative ChIP\-Seq, the features might be binding region from a</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">pre\-determined list.</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">.sp</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">Special care must be taken to decide how to deal with reads that overlap more</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">than one feature. The \fBhtseq\-count\fP script allows one to choose between three</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">modes. Of course, if none of these fits your needs, you can write your own</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">script with HTSeq. See the chapter tour for a step\-by\-step guide on</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">how to do so. See also the FAQ at the end, if the following explanation seems</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">to technical.</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">.sp</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">The three overlap resolution modes of \fBhtseq\-count\fP work as follows. For</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">each position \fIi\fP in the read, a set \fIS(i)\fP is defined as the set of all</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">features overlapping position \fIi\fP\&. Then, consider the set \fIS\fP, which is</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">(with \fIi\fP running through all position within the read or a read pair)</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">.INDENT 0.0</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">.IP \(bu 2</span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">the union of all the sets \fIS(i)\fP for mode \fBunion\fP\&. This mode is recommended for most use cases.</span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">.IP \(bu 2</span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">the intersection of all the sets \fIS(i)\fP for mode \fBintersection\-strict\fP\&.</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">.IP \(bu 2</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">the intersection of all non\-empty sets \fIS(i)\fP for mode \fBintersection\-nonempty\fP\&.</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">.UNINDENT</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">.sp</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">If \fIS\fP contains precisely one feature, the read (or read pair) is counted for this feature. If</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">it contains more than one feature, the read (or read pair) is counted as \fBambiguous\fP (and</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">not counted for any features), and if \fBS\fP is empty, the read (or read pair) is counted</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext">as \fBno_feature\fP\&.</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">.sp</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext">The following figure illustrates the effect of these three modes:</span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext">[image]</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">.SH USAGE</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext">.sp</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext">After you have installed HTSeq (see install), you can run \fBhtseq\-count\fP from</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext">the command line:</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext">.INDENT 0.0</span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext">.INDENT 3.5</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext">.sp</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext">.nf</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext">.ft C</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext">htseq\-count [options] <alignment_file> <gff_file></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext">.ft P</span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext">.fi</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext">.UNINDENT</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext">.UNINDENT</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext">.sp</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext">If the file \fBhtseq\-qa\fP is not in your path, you can, alternatively, call the script with</span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext">.INDENT 0.0</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext">.INDENT 3.5</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext">.sp</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext">.nf</span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext">.ft C</span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext">python \-m HTSeq.scripts.count [options] <alignment_file> <gff_file></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext">.ft P</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext">.fi</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext">.UNINDENT</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext">.UNINDENT</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext">.sp</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext">The \fB<alignment_file>\fP contains the aligned reads in the SAM format. (Note that the</span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext">\fI\%SAMtools\fP contain Perl scripts to convert most alignment formats to SAM.)</span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext">Make sure to use a splicing\-aware aligner such as TopHat. HTSeq\-count makes</span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext">full use of the information in the CIGAR field.</span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext">.sp</span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext">To read from standard input, use \fB\-\fP as \fB<alignment_file>\fP\&.</span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext">.sp</span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext">If you have paired\-end data, pay attention to the \fB\-r\fP option described below.</span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext">.sp</span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext">The \fB<gff_file>\fP contains the features in the \fI\%GFF format\fP\&.</span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext">.sp</span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext">The script outputs a table with counts for each feature, followed by</span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext">the special counters, which count reads that were not counted for any feature</span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext">for various reasons. The names of the special counters all start with</span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext">a double underscore, to facilitate filtering. (Note: The double unscore</span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext">was absent up to version 0.5.4). The special counters are:</span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext">.INDENT 0.0</span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext">.IP \(bu 2</span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext">\fB__no_feature\fP: reads (or read pairs) which could not be assigned to any feature</span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext">(set \fIS\fP as described above was empty).</span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext">.IP \(bu 2</span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext">\fB__ambiguous\fP: reads (or read pairs) which could have been assigned to more than</span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="plaintext">one feature and hence were not counted for any of these (set \fIS\fP</span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext">had more than one element).</span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext">.IP \(bu 2</span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="plaintext">\fB__too_low_aQual\fP: reads (or read pairs) which were skipped due to the \fB\-a\fP</span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="plaintext">option, see below</span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="plaintext">.IP \(bu 2</span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="plaintext">\fB__not_aligned\fP: reads (or read pairs) in the SAM file without alignment</span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="plaintext">.IP \(bu 2</span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="plaintext">\fB__alignment_not_unique\fP: reads (or read pairs) with more than one reported alignment.</span>
</pre>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="plaintext">These reads are recognized from the \fBNH\fP optional SAM field tag.</span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="plaintext">(If the aligner does not set this field, multiply aligned reads will</span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="plaintext">be counted multiple times, unless they getv filtered out by due to the \fB\-a\fP option.)</span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext">.UNINDENT</span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="plaintext">.sp</span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="plaintext">\fIImportant:\fP The default for strandedness is \fIyes\fP\&. If your RNA\-Seq data has not been made</span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="plaintext">with a strand\-specific protocol, this causes half of the reads to be lost.</span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="plaintext">Hence, make sure to set the option \fB\-\-stranded=no\fP unless you have strand\-specific</span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="plaintext">data!</span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="plaintext">.SS Options</span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="plaintext">.INDENT 0.0</span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="plaintext">.TP</span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="plaintext">.B \-f <format>, \-\-format=<format></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="plaintext">Format of the input data. Possible values are \fBsam\fP (for text SAM files)</span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="plaintext">and \fBbam\fP (for binary BAM files). Default is \fBsam\fP\&.</span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="plaintext">.UNINDENT</span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="plaintext">.INDENT 0.0</span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="plaintext">.TP</span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="plaintext">.B \-r <order>, \-\-order=<order></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="plaintext">For paired\-end data, the alignment have to be sorted either by read name or</span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="plaintext">by alignment position. If your data is not sorted, use the \fBsamtools sort\fP</span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="plaintext">function of \fBsamtools\fP to sort it. Use this option, with \fBname\fP or \fBpos\fP</span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="plaintext">for \fB<order>\fP to indicate how the input data has been sorted. The default</span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="plaintext">is \fBname\fP\&.</span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="plaintext">.sp</span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="plaintext">If \fBname\fP is indicated, \fBhtseq\-count\fP expects all the alignments for the</span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="plaintext">reads of a given read pair to appear in adjacent records in the input data.</span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="plaintext">For \fBpos\fP, this is not expected; rather, read alignments whose mate alignment</span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="plaintext">have not yet been seen are kept in a buffer in memory until the mate is found.</span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="plaintext">While, strictly speaking, the latter will also work with unsorted data, sorting</span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="plaintext">ensures that most alignment mates appear close to each other in the data</span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="plaintext">and hence the buffer is much less likely to overflow.</span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="plaintext">.UNINDENT</span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="plaintext">.INDENT 0.0</span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="plaintext">.TP</span>
</pre>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="plaintext">.B \-s <yes/no/reverse>, \-\-stranded=<yes/no/reverse></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="plaintext">whether the data is from a strand\-specific assay (default: \fByes\fP)</span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="plaintext">.sp</span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="plaintext">For \fBstranded=no\fP, a read is considered overlapping with a feature regardless</span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="plaintext">of whether it is mapped to the same or the opposite strand as the feature.</span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="plaintext">For \fBstranded=yes\fP and single\-end reads, the read has to be mapped to the same</span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="plaintext">strand as the feature. For paired\-end reads, the first</span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="plaintext">read has to be on the same strand and the second read on the opposite strand.</span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="plaintext">For \fBstranded=reverse\fP, these rules are reversed.</span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="plaintext">.UNINDENT</span>
</pre>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="plaintext">.INDENT 0.0</span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="plaintext">.B \-a <minaqual>, \-\-a=<minaqual></span>
</pre>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="plaintext">skip all reads with alignment quality lower than the given</span>
</pre>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="plaintext">minimum value (default: 10 — Note: the default used to be 0 until</span>
</pre>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="plaintext">version 0.5.4.)</span>
</pre>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="plaintext">.UNINDENT</span>
</pre>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="plaintext">.INDENT 0.0</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="plaintext">.TP</span>
</pre>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="plaintext">.B \-t <feature type>, \-\-type=<feature type></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="plaintext">feature type (3rd column in GFF file) to be used, all</span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="plaintext">features of other type are ignored (default, suitable</span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="plaintext">for RNA\-Seq analysis using an \fI\%Ensembl GTF\fP file: \fBexon\fP)</span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="plaintext">.UNINDENT</span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="plaintext">.INDENT 0.0</span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="plaintext">.TP</span>
</pre>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="plaintext">.B \-i <id attribute>, \-\-idattr=<id attribute></span>
</pre>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="plaintext">GFF attribute to be used as feature ID. Several GFF lines with the same</span>
</pre>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="plaintext">feature ID will be considered as parts of the same feature. The feature ID</span>
</pre>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="plaintext">is used to identity the counts in the output table. The default, suitable</span>
</pre>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="plaintext">for RNA\-Seq analysis using an Ensembl GTF file, is \fBgene_id\fP\&.</span>
</pre>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="plaintext">.UNINDENT</span>
</pre>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="plaintext">.INDENT 0.0</span>
</pre>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="plaintext">.TP</span>
</pre>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="plaintext">.B \-m <mode>, \-\-mode=<mode></span>
</pre>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="plaintext">Mode to handle reads overlapping more than one feature. Possible values for</span>
</pre>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="plaintext">\fI<mode>\fP are \fBunion\fP, \fBintersection\-strict\fP and \fBintersection\-nonempty\fP</span>
</pre>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="plaintext">(default: \fBunion\fP)</span>
</pre>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="plaintext">.UNINDENT</span>
</pre>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="plaintext">.INDENT 0.0</span>
</pre>
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206
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<pre style="margin: 0;">+<span id="LC206" 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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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="plaintext">.B \-o <samout>, \-\-samout=<samout></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="plaintext">write out all SAM alignment records into an output SAM</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="plaintext">file called <samout>, annotating each line with its</span>
</pre>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="plaintext">assignment to a feature or a special counter</span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="plaintext">(as an optional field with tag ‘XF’)</span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="plaintext">.UNINDENT</span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="plaintext">.INDENT 0.0</span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="plaintext">.TP</span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="plaintext">.B \-q, \-\-quiet</span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="plaintext">suppress progress report and warnings</span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="plaintext">.UNINDENT</span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="plaintext">.INDENT 0.0</span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="plaintext">.TP</span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="plaintext">.B \-h, \-\-help</span>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="plaintext">Show a usage summary and exit</span>
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222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="plaintext">.UNINDENT</span>
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223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="plaintext">.SS Frequenctly asked questions</span>
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224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="plaintext">.INDENT 0.0</span>
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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="plaintext">.TP</span>
</pre>
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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="plaintext">.B \fIMy shell reports “command not found” when I try to run “htseq\-count”. How can I launch the script?\fP</span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="plaintext">The file “htseq\-count” has to be in the system’s \fI\%search path\fP\&. By default, Python places it</span>
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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="plaintext">in its script directory, which you have to add to your search path. A maybe easier alternative</span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="plaintext">is to write \fBpython \-m HTSeq.scripts.count\fP instead of \fBhtseq\-count\fP, followed by the</span>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="plaintext">options and arguments, which will launch the htseq\-count script as well.</span>
</pre>
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231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="plaintext">.UNINDENT</span>
</pre>
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232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="plaintext">.INDENT 0.0</span>
</pre>
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233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="plaintext">.TP</span>
</pre>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="plaintext">.B \fIWhy are multi\-mapping reads and reads overlapping multiple features discarded rather than counted for each feature?\fP</span>
</pre>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="plaintext">The primary intended use case for \fBhtseq\-count\fP is \fIdifferential\fP expression analysis, where</span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="plaintext">one compares the expression of the same gene across samples and not the expression of different</span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="plaintext">genes within a sample. Now, consider two genes, which share a stretch of common sequence</span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="plaintext">such that for a read mapping to this stretch, the aligner cannot decide which of the two genes</span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="plaintext">the read originated from and hence reports a multiple alignment. If we discard all such reads,</span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="plaintext">we undercount the total output of the genes, but the \fIratio\fP of expression strength (the “fold</span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="plaintext">change”) between samples or experimental condition will still be correct, because we discard the</span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="plaintext">same fratcion of reads in all samples. On the other hand, if we counted these reads for both</span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="plaintext">genes, a subsequent diffential\-expression analysis might find false positives: Even if only one of the</span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="plaintext">gene changes increases its expression in reaction to treatment, the additional read caused by this</span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="plaintext">would be counted for both genes, giving the wrong appearance that both genes reacted to the treatment.</span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="plaintext">.B \fII have used a GTF file generated by the Table Browser function of the UCSC Genome Browser, and most reads are counted as ambiguous. Why?\fP</span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="plaintext">In these files, the \fBgene_id\fP attribute incorrectly contains the same value as the \fBtranscript_id\fP</span>
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="plaintext">attribute and hence a different value for each transcript of the same gene. Hence, if a read maps to</span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="plaintext">an exon shared by several transcripts of the same gene, this will appear to \fBhtseq\-count\fP as and</span>
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="plaintext">overlap with several genes. Therefore, these GTF files cannot be used as is. Either correct the</span>
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="plaintext">incorrect \fBgene_id\fP attributes with a suitable script, or use a GTF file from a different source.</span>
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="plaintext">.B \fICan I use htseq\-count to count reads mapping to transcripts rather than genes?\fP</span>
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="plaintext">In principle, you could instruct htseq\-count to count for each of a gene’s transcript individually, by</span>
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="plaintext">specifying \fB\-\-idattr transcript_id\fP\&. However, all reads mapping to exons shared by several</span>
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="plaintext">transcripts will then be considered ambiguous. (See second question.) Counting them for each transcript</span>
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="plaintext">that contains the exons would be possible but makes little sense for typical use cases. (See first</span>
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="plaintext">question.) If you want to perform differential expression analysis on the level of</span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="plaintext">individual transcripts, maybe ahve a look at \fI\%our paper on DEXSeq\fP for a discussion on why we</span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="plaintext">prefer performing such analyses on the level of exons instead.</span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="plaintext">.UNINDENT</span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="plaintext">.INDENT 0.0</span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="plaintext">.TP</span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="plaintext">.B \fIFor paired\-end data, does htseq\-count count reads or read pairs?\fP</span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="plaintext">Read pairs. The script is designed to count “units of evidence” for gene expression. If both mates map</span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="plaintext">to the same gene, this still only shows that one cDNA fragment originated from that gene. Hence, it</span>
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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="plaintext">should be counted only once.</span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="plaintext">.TP</span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="plaintext">.B \fIWhat happens if the two reads in a pair overlap two different features?\fP</span>
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="plaintext">The same as if one read overlaps two features: The read or read pair is counted as ambiguous.</span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="plaintext">.TP</span>
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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="plaintext">.B \fIWhat happened if the mate of an aligned read is not aligned?\fP</span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="plaintext">For the default mode “union”, only the aligned read determines how the read pair is counted. For the</span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="plaintext">other modes, see their description.</span>
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="plaintext">.TP</span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="plaintext">.B \fIMost of my RNA\-Seq reads are counted as \(ga\(ga__no_feature\(ga\(ga. What could have gone wrong?\fP</span>
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278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="plaintext">Common causes include:</span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="plaintext">\- The \fB\-\-stranded\fP option was set wrongly. Use a genome browser (e.g., IGV) to check.</span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="plaintext">\- The GTF file uses coordinates from another reference assembly as the SAM file.</span>
</pre>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="plaintext">\- The chromosome names differ between GTF and SAM file (e.g., \fBchr1\fP in one file and jsut \fB1\fP in the other).</span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="plaintext">.TP</span>
</pre>
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="plaintext">.B \fIWhich overlap mode should I use?\fP</span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="plaintext">When I wrote \fBhtseq\-count\fP, I was not sure which option is best and included three possibilities. Now,</span>
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="plaintext">several years later, I have seen very few cases where the default \fBunion\fP would not be appropriate</span>
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="plaintext">and hence tend to recommend to just stick to \fBunion\fP\&.</span>
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="plaintext">.B \fII have a GTF file? How do I convert it to GFF?\fP</span>
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="plaintext">No need to do that, because GTF is a tightening of the GFF format. Hence, all GTF files are GFF files, too.</span>
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="plaintext">By default, htseq\-count expects a GTF file.</span>
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="plaintext">.B \fII have a GFF file, not a GTF file. How can I use it to count RNA\-Seq reads?\fP</span>
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="plaintext">The GTF format specifies, inter alia, that exons are marked by the word \fBexon\fP in the third column and</span>
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="plaintext">that the gene ID is given in an attribute named \fBgene_id\fP, and htseq\-count expects these words to be used</span>
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="plaintext">by default. If you GFF file uses a word other than \fBexon\fP in its third column to mark lines describing</span>
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="plaintext">exons, notify \fBhtseq\-count\fP using the \fB\-\-type\fP option. If the name of the attribute containing the</span>
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="plaintext">gene ID for exon lines is not \fBgene_id\fP, use the \fB\-\-idattr\fP\&. Often, its is, for example,</span>
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="plaintext">\fBParent\fP, \fBGeneID\fP or \fBID\fP\&. Make sure it is the gene ID and not the exon ID.</span>
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="plaintext">.B \fIHow can I count overlaps with features other than genes/exons?\fP</span>
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="plaintext">If you have GFF file listing your features, use it together with the \fB\-\-type\fP and \fB\-\-idattr\fP options.</span>
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="plaintext">If your feature intervals need to be computed, you are probably better off writing your own</span>
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="plaintext">counting script (provided you have some knowledge of Python). Follow the tutorial in the other pages</span>
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="plaintext">of this documentation to see how to use HTSeq for this.</span>
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="plaintext">.B \fIHow should I cite htseq\-count in a publication?\fP</span>
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="plaintext">Please cite HTSeq as follows: S Anders, T P Pyl, W Huber: \fIHTSeq — A Python framework to work with</span>
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="plaintext">high\-throughput sequencing data\fP\&. bioRxiv 2014. \fI\%doi: 10.1101/002824\fP\&.</span>
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="plaintext">(This is a preprint currently under review. We will replace this with the reference to the final</span>
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310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="plaintext">published version once available.)</span>
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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="plaintext">.UNINDENT</span>
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312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="plaintext">.SH AUTHOR</span>
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313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="plaintext">Simon Anders</span>
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314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="plaintext">.SH COPYRIGHT</span>
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315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="plaintext">2017, Simon Anders</span>
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316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="plaintext">.\" Generated by docutils manpage writer.</span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="plaintext">.</span></pre>
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<li id="a18e68093b9966efb5679aea8d79db88105c7396">
<a href="https://salsa.debian.org/med-team/htseq/compare/1a15a0f9fdf71bda8cfc3359ccba32da18a556af...ca6807052dce671b9c96149b9c0468f9826ef5b4#a18e68093b9966efb5679aea8d79db88105c7396"><strong>debian/man/htseq-qa.1</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.\" Man page generated from reStructuredText.</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">.TH "HTSEQ-QA" "1" "Oct 01, 2017" "0.6.1p1" "HTSeq"</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">htseq-qa \- Perform simple quality assessment of high-throughput sequencing reads</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">.</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">.nr rst2man-indent-level 0</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">.</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">.de1 rstReportMargin</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">\\$1 \\n[an-margin]</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">level \\n[rst2man-indent-level]</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">level margin: \\n[rst2man-indent\\n[rst2man-indent-level]]</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">-</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">\\n[rst2man-indent0]</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">\\n[rst2man-indent1]</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">\\n[rst2man-indent2]</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">..</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">.de1 INDENT</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">.\" .rstReportMargin pre:</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">. RS \\$1</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">. nr rst2man-indent\\n[rst2man-indent-level] \\n[an-margin]</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">. nr rst2man-indent-level +1</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">.\" .rstReportMargin post:</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">..</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">.de UNINDENT</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">. RE</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">.\" indent \\n[an-margin]</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">.\" old: \\n[rst2man-indent\\n[rst2man-indent-level]]</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">.nr rst2man-indent-level -1</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">.\" new: \\n[rst2man-indent\\n[rst2man-indent-level]]</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">.in \\n[rst2man-indent\\n[rst2man-indent-level]]u</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">..</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">.sp</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">The Python script \fBhtseq\-qa\fP takes a file with sequencing reads (either</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">raw or aligned reads) and produces a PDF file with useful plots to assess</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">the technical quality of a run.</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">.SH PLOT</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">.sp</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">Here is a typical plot:</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">[image]</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">.sp</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">The plot is made from a SAM file, which contained aligned and unalignable reads.</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">The left column is made from the non\-aligned, the right column from the aligned</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">reads. The header informs you about the name of the SAM file, and the number of</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">reads.</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">.sp</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">The upper row shows how often which base was called for each position in the</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">read. In this sample, the non\-alignable reads have a clear excess in A. The</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">aligned reads have a balance between complementing reads: A and C (reddish colours)</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">have equal levels, and so do C and G (greenish colours). The sequences seem to be AT</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">rich. Furthermore, nearly all aligned reads start with a T, followed by an A, and then,</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">a C in 70% and an A in 30% of the reads. Such an imbalance would be reason for concern</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">if it has no good explanation. Here, the reason is that the fragmentation of the sample</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">was done by enzyme digestion.</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">.sp</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">The lower half shows the abundance of base\-call quality scores at the different positions</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">in the read. Nearly all aligned reads have a quality of 34 over their whole length, while</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">for the non\-aligned reads, some reads have lower quality scores towards their ends.</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">.SH USAGE</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">.sp</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">Note that \fBhtseq\-qa\fP needs matplotlib to produce the plot, so you need to install this</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">module, as described \fI\%here\fP on the matplotlib web site.</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">.sp</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">After you have installed HTSeq (see install) and matplotlib, you can run \fBhtseq\-qa\fP from</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">the command line:</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">.INDENT 0.0</span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">.INDENT 3.5</span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">.sp</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext">.nf</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">.ft C</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext">htseq\-qa [options] read_file</span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext">.ft P</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">.fi</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext">.UNINDENT</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext">.UNINDENT</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext">.sp</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext">If the file \fBhtseq\-qa\fP is not in your path, you can, alternatively, call the script with</span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext">.INDENT 0.0</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext">.INDENT 3.5</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext">.sp</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext">.nf</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext">.ft C</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext">python \-m HTSeq.scripts.qa [options] read_file</span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext">.ft P</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext">.fi</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext">.UNINDENT</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext">.UNINDENT</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext">.sp</span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext">The \fIread_file\fP is either a FASTQ file or a SAM file. For a SAM file, a plot with two columns</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext">is produced as above, for a FASTQ file, you get only one column.</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext">.sp</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext">The output is written into a file with the same name as \fIread_file\fP, with the suffix \fB\&.pdf\fP</span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext">added. View it with a PDF viewer such as the Acrobat Reader.</span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext">.SS Options</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext">.INDENT 0.0</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext">.TP</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext">.B \-t <type>, \-\-type=<type></span>
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<td class="diff-line-num new new_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
98
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext">The file type of the \fIread_file\fP\&. Supported values for \fI<type>\fP are:</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext">.INDENT 7.0</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext">.IP \(bu 2</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="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext">\fBsam\fP: a SAM file (Note that the \fI\%SAMtools\fP contain Perl scripts to convert</span>
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<td class="diff-line-num new new_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext">most alignment formats to SAM)</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext">.IP \(bu 2</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext">\fBsolexa\-export\fP: an \fB_export.txt\fP file as produced by the SolexaPipeline</span>
</pre>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext">software after aligning with Eland (\fBhtseq\-qa\fP expects the new Solexa quality</span>
</pre>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext">encoding as produced by version 1.3 or newer of the SolexaPipeline)</span>
</pre>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext">.IP \(bu 2</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext">\fBfastq\fP: a FASTQ file with standard (Sanger or Phred) quality encoding</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext">.IP \(bu 2</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext">\fBsolexa\-fastq\fP: a FASTQ file with Solexa quality encoding, as produced by</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="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext">the SolexaPipeline after base\-calling with Bustard (\fBhtseq\-qa\fP expects</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="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext">the new Solexa quality encoding as produced by version 1.3 or newer</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext">of the SolexaPipeline)</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext">.UNINDENT</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="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext">.UNINDENT</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="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext">.INDENT 0.0</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="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="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext">.B \-o <outfile>, \-\-outfile=<outfile></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
119
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext">output filename (default is \fI<read_file>\(ga\(ga\fP\&.pdf\(ga\(ga)</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
120
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext">.UNINDENT</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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121
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext">.INDENT 0.0</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="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
122
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC122" 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="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
123
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext">.B \-r <readlen>, \-\-readlength=<readlen></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="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
124
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext">the maximum read length (when not specified, the</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="plaintext">script guesses from the 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="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
126
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC126" class="line" lang="plaintext">.UNINDENT</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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127
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC127" class="line" lang="plaintext">.INDENT 0.0</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="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
128
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC128" 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="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
129
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC129" class="line" lang="plaintext">.B \-g <gamma>, \-\-gamma=<gamma></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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130
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC130" class="line" lang="plaintext">the gamma factor for the contrast adjustment of the</span>
</pre>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="plaintext">quality score plot</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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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="plaintext">.UNINDENT</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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133
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC133" class="line" lang="plaintext">.INDENT 0.0</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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134
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext">.TP</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="plaintext">.B \-n, \-\-nosplit</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="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
136
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC136" class="line" lang="plaintext">do not split reads in unaligned and aligned ones, i.e., produce</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="plaintext">a one\-column plot</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="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
138
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC138" class="line" lang="plaintext">.UNINDENT</span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
139
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC139" class="line" lang="plaintext">.INDENT 0.0</span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
140
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC140" class="line" lang="plaintext">.TP</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
141
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC141" class="line" lang="plaintext">.B \-m, \-\-maxqual</span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
142
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC142" class="line" lang="plaintext">the maximum quality score that appears in the data (default: 40)</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="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
143
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC143" class="line" lang="plaintext">.UNINDENT</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="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="plaintext">.INDENT 0.0</span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="plaintext">.TP</span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="plaintext">.B \-h, \-\-help</span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="plaintext">Show a usage summary and exit</span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="plaintext">.UNINDENT</span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="plaintext">.SH AUTHOR</span>
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<td class="diff-line-num new new_line" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="plaintext">Simon Anders</span>
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<td class="diff-line-num new new_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="plaintext">.SH COPYRIGHT</span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="plaintext">2017, Simon Anders</span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="plaintext">.\" Generated by docutils manpage writer.</span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="plaintext">.</span></pre>
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<li id="f5bb5c2f86e675f64484fae13f789f4c43d473aa">
<a href="https://salsa.debian.org/med-team/htseq/compare/1a15a0f9fdf71bda8cfc3359ccba32da18a556af...ca6807052dce671b9c96149b9c0468f9826ef5b4#f5bb5c2f86e675f64484fae13f789f4c43d473aa"><strong>debian/python3-htseq.manpages</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/man/*</span></pre>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/htseq/compare/1a15a0f9fdf71bda8cfc3359ccba32da18a556af...ca6807052dce671b9c96149b9c0468f9826ef5b4#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,6 +5,8 @@ export PYBUILD_NAME=htseq</td>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"># see https://wiki.debian.org/Python/LibraryStyleGuide</span>
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">export http_proxy=http://127.0.9.1:9</span>
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7
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">export DEB_BUILD_MAINT_OPTIONS=hardening=+all</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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8
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">%:</span>
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9
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> dh $@ --with python2,python3 --buildsystem=pybuild</span>
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10
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -15,3 +17,8 @@ override_dh_auto_clean:</td>
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15
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> for link in 'src' 'HTSeq' 'doc' 'scripts' 'test' ; do \</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> if [ -L $${link} ] ; then rm $${link} ; fi \</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> done</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">override_dh_install:</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> dh_install</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> # binaries should be only in python3 package</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> rm -rf debian/python-$(PYBUILD_NAME)/usr/bin</span></pre>
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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">\ No newline at end of file</td>
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<a href="https://salsa.debian.org/med-team/htseq/compare/1a15a0f9fdf71bda8cfc3359ccba32da18a556af...ca6807052dce671b9c96149b9c0468f9826ef5b4#68ef9f98c01c7eecd4c605cc26048a06f3304b79"><strong>debian/watch</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">version=<span class="idiff left right">3</span></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">http<span class="idiff left right">://pypi.debian.net/HTSeq/HTSeq-([0-9.p]*)\.tar\.gz</span></span></pre>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">version=<span class="idiff left right">4</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">http<span class="idiff left right">s://pypi.python.org/pypi/HTSeq .*/HTSeq@ANY_VERSION@@ARCHIVE_EXT@</span></span></pre>
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