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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/chip-seq">Debian Med / chip-seq</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/chip-seq/-/commit/f79f7d439b09512444c534d340e425a007ebf20e">f79f7d43</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-03-24T21:21:02+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Only one patch for Makefile, propagate hardening flags, add autopkgtest
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/chip-seq/-/commit/c47742f849c78495d01ec03c150af34aa100219a">c47742f8</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-03-24T21:31:55+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add lintian override
</pre>
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<h4>8 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9a14945e16c9144bd18a7ed182b1f8e4a2b50d7c">
<span class="new-file">
+
debian/examples
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</li>
<li class="file-stats">
<a href="#efc7fe57b5983b0283c6410fceef7e74f687aeb5">
<span class="new-file">
+
debian/lintian-overrides
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<li class="file-stats">
<a href="#af5e13ec7db0b92fee10569b5904cd0fb8b966a6">
<span class="deleted-file">
−
debian/patches/fix_install.patch
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<li class="file-stats">
<a href="#ec929ef01d1cf2a9933f4a573f16144feabcf330">
debian/patches/fix_linker.patch
→
debian/patches/fix_makefile.patch
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#86f43a8ebc331d59bcdd86d371c7a6393c81b8c1">
<span class="new-file">
+
debian/tests/H3K4me3.sga
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<li class="file-stats">
<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
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+
debian/tests/control
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<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<span class="new-file">
+
debian/tests/run-unit-test
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<h4>Changes:</h4>
<li id="9a14945e16c9144bd18a7ed182b1f8e4a2b50d7c">
<a href="https://salsa.debian.org/med-team/chip-seq/-/compare/5934d18d1ef0c9298cc9e9d77caccbab0b9d9e2e...c47742f849c78495d01ec03c150af34aa100219a#9a14945e16c9144bd18a7ed182b1f8e4a2b50d7c"><strong>debian/examples</strong></a>
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<td class="diff-line-num new new_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/tests/*.sga</span></pre>
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<li id="efc7fe57b5983b0283c6410fceef7e74f687aeb5">
<a href="https://salsa.debian.org/med-team/chip-seq/-/compare/5934d18d1ef0c9298cc9e9d77caccbab0b9d9e2e...c47742f849c78495d01ec03c150af34aa100219a#efc7fe57b5983b0283c6410fceef7e74f687aeb5"><strong>debian/lintian-overrides</strong></a>
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<td class="diff-line-num new new_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"># see https://lists.debian.org/debian-med/2018/06/msg00043.html</span>
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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">chip-seq: script-with-language-extension usr/bin/*.*</span></pre>
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<li id="af5e13ec7db0b92fee10569b5904cd0fb8b966a6">
<a href="https://salsa.debian.org/med-team/chip-seq/-/compare/5934d18d1ef0c9298cc9e9d77caccbab0b9d9e2e...c47742f849c78495d01ec03c150af34aa100219a#af5e13ec7db0b92fee10569b5904cd0fb8b966a6"><strong>debian/patches/fix_install.patch</strong>
deleted
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Mon, 23 Mar 2020 20:55:38 +0100</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Description: Fix install dir</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff">--- a/Makefile</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/Makefile</span></span>
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<td class="diff-line-num old old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="p">@@ -10,7 +10,7 @@</span> LDFLAGS += -O3 -std=gnu99 -fPIC -lm</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"> #binDir = $(PWD)/bin</span>
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<td class="diff-line-num old old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"> #manDir = /usr/share/man/man1/</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"> ifeq ($(prefix),)</span>
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<td class="diff-line-num old old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- prefix := $(DESTDIR).</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ prefix := $(DESTDIR)</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"> endif</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"> binDir = $(prefix)/bin</span>
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<td class="diff-line-num old old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"> datDir = $(prefix)/share/chip-seq</span></pre>
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<li id="ec929ef01d1cf2a9933f4a573f16144feabcf330">
<a href="https://salsa.debian.org/med-team/chip-seq/-/compare/5934d18d1ef0c9298cc9e9d77caccbab0b9d9e2e...c47742f849c78495d01ec03c150af34aa100219a#ec929ef01d1cf2a9933f4a573f16144feabcf330"><strong>debian/patches/fix_linker.patch</strong>
→
<strong>debian/patches/fix_makefile.patch</strong>
</a>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,15 +4,25 @@ Description: Fix linker flags</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff">--- a/Makefile</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="p">@@ -3,7 +3,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -2,15 +2,15 @@</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> # Makefile for ChIP-Seq package</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"> #</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"> CC = gcc</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"><span class="idiff left right"> </span>CFLAGS = -O3 -std=gnu99 -W -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;"><span class="idiff left right">-</span>CFLAGS = -O3 -std=gnu99 -W -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-LDFLAGS = -O3 -std=gnu99 -fPIC -lm</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+CFLAGS += -O3 -std=gnu99 -W -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+LDFLAGS += -O3 -std=gnu99 -fPIC -lm</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"> #CFLAGS = -O3 -std=gnu99 -W -pedantic</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="diff"> #LDFLAGS = -O3 -std=gnu99 -fPIC -lm</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> #binDir = $(PWD)/bin</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> #manDir = /usr/share/man/man1/</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> ifeq ($(prefix),)</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- prefix := $(DESTDIR).</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ prefix := $(DESTDIR)</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> endif</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> binDir = $(prefix)/bin</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> datDir = $(prefix)/share/chip-seq</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="diff"><span class="p">@@ -77,16 +77,16 @@</span> tools/filter_counts : $(FILTER_COUNTS_SR</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="diff"> $(CC) $(CFLAGS) -o tools/filter_counts $^</span>
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18
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28
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="diff"> </span>
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<a href="https://salsa.debian.org/med-team/chip-seq/-/compare/5934d18d1ef0c9298cc9e9d77caccbab0b9d9e2e...c47742f849c78495d01ec03c150af34aa100219a#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">fix_<span class="idiff left right">linker</span>.patch</span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">fix_install.patch</span></pre>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">fix_<span class="idiff left right">makefile</span>.patch</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"><span class="idiff left right"># </span>fix_install.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/chip-seq/-/compare/5934d18d1ef0c9298cc9e9d77caccbab0b9d9e2e...c47742f849c78495d01ec03c150af34aa100219a#86f43a8ebc331d59bcdd86d371c7a6393c81b8c1"><strong>debian/tests/H3K4me3.sga</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">NC_000001.9 H3K4me3 4794 + 1</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">NC_000001.9 H3K4me3 6090 + 1</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">NC_000001.9 H3K4me3 6099 + 1</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">NC_000001.9 H3K4me3 6655 + 1</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">NC_000001.9 H3K4me3 18453 - 1</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">NC_000001.9 H3K4me3 19285 + 1</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">NC_000001.9 H3K4me3 44529 + 1</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">NC_000001.9 H3K4me3 46333 + 1</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">NC_000001.9 H3K4me3 46349 - 1</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">NC_000001.9 H3K4me3 52929 + 1</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">NC_000001.9 H3K4me3 59412 + 1</span></pre>
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<a href="https://salsa.debian.org/med-team/chip-seq/-/compare/5934d18d1ef0c9298cc9e9d77caccbab0b9d9e2e...c47742f849c78495d01ec03c150af34aa100219a#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Tests: run-unit-test</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Depends: @</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Restrictions: allow-stderr</span></pre>
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<a href="https://salsa.debian.org/med-team/chip-seq/-/compare/5934d18d1ef0c9298cc9e9d77caccbab0b9d9e2e...c47742f849c78495d01ec03c150af34aa100219a#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="nv" style="color: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span>chip-seq</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">LC_ALL</span><span class="o" style="font-weight: 600;">=</span>C.UTF-8</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="si" style="color: #d14;">)</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># Double quote below to expand the temporary directory variable now versus</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># later is on purpose.</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># shellcheck disable=SC2064</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/examples/<span class="k" style="font-weight: 600;">*</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell">chipcor <span class="nt" style="color: #000080;">-A</span> <span class="s2" style="color: #d14;">"H3K4me3 +"</span> <span class="nt" style="color: #000080;">-B</span> <span class="s2" style="color: #d14;">"H3K4me3 -"</span> <span class="nt" style="color: #000080;">-b</span> <span class="nt" style="color: #000080;">-1000</span> <span class="nt" style="color: #000080;">-e</span> 1000 <span class="nt" style="color: #000080;">-w</span> 1 <span class="nt" style="color: #000080;">-c</span> 20 <span class="nt" style="color: #000080;">-n</span> 1 H3K4me3.sga <span class="o" style="font-weight: 600;">></span> H3K4me3_fc_n1.out</span></pre>
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