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<h3>
Shayan Doust pushed to branch master
at <a href="https://salsa.debian.org/med-team/covtobed">Debian Med / covtobed</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/covtobed/-/commit/1a7224f5bfb7fc2cd3765df464da9cfb9fb1ff6b">1a7224f5</a></strong>
<div>
<span>by Shayan Doust</span>
<i>at 2020-06-04T13:27:51+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add more example data to covtobed-examples
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<li>
<strong><a href="https://salsa.debian.org/med-team/covtobed/-/commit/f173df5696a49a31b75bebb2dbab036e405daf29">f173df56</a></strong>
<div>
<span>by Shayan Doust</span>
<i>at 2020-06-04T13:39:11+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Patch test script so it uses covtobed binary installed on system and works with autopkgtest
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<h4>3 changed files:</h4>
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<a href="#cb426256cd4b9c0a6650af21a1e7f0491e87b4ca">
debian/covtobed-examples.install
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<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
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+
debian/patches/series
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<li class="file-stats">
<a href="#a53adf029254e0148bed48d71f6702649066310d">
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+
debian/patches/test_use_system_installed_binary.patch
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<h4>Changes:</h4>
<li id="cb426256cd4b9c0a6650af21a1e7f0491e87b4ca">
<a href="https://salsa.debian.org/med-team/covtobed/-/compare/b3e2773294ecb4ac8daacc4b597e3c025b64e73d...f173df5696a49a31b75bebb2dbab036e405daf29#cb426256cd4b9c0a6650af21a1e7f0491e87b4ca"><strong>debian/covtobed-examples.install</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="php"><span class="nx">test</span><span class="o" style="font-weight: 600;">/</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">doc</span><span class="o" style="font-weight: 600;">/</span><span class="nx">covtobed</span><span class="o" style="font-weight: 600;">-</span><span class="nx">examples</span><span class="o" style="font-weight: 600;">/</span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nx">test</span><span class="o" style="font-weight: 600;">/*</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">doc</span><span class="o" style="font-weight: 600;">/</span><span class="nx">covtobed</span><span class="o" style="font-weight: 600;">-</span><span class="nx">examples</span><span class="o" style="font-weight: 600;">/</span><span class="nx">examples</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="php"><span class="nx">example_data</span><span class="o" style="font-weight: 600;">/*</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">doc</span><span class="o" style="font-weight: 600;">/</span><span class="nx">covtobed</span><span class="o" style="font-weight: 600;">-</span><span class="nx">examples</span><span class="o" style="font-weight: 600;">/</span><span class="nx">examples</span></span></pre>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/covtobed/-/compare/b3e2773294ecb4ac8daacc4b597e3c025b64e73d...f173df5696a49a31b75bebb2dbab036e405daf29#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">test_use_system_installed_binary.patch</span></pre>
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<li id="a53adf029254e0148bed48d71f6702649066310d">
<a href="https://salsa.debian.org/med-team/covtobed/-/compare/b3e2773294ecb4ac8daacc4b597e3c025b64e73d...f173df5696a49a31b75bebb2dbab036e405daf29#a53adf029254e0148bed48d71f6702649066310d"><strong>debian/patches/test_use_system_installed_binary.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: modify test script so it works with autopkgtest</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Author: Shayan Doust <hello@shayandoust.me></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Last-Update: 2020-06-04</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">---</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- covtobed.orig/test/test.sh</span></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;">+++ covtobed/test/test.sh</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -7,40 +7,20 @@</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> # ./test/mock.bam</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"> REMOVE=0</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-if [ ! -e "test/demo.bam" ]; then</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;">- echo "WARNING: running this test from a bad location"</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null && pwd )"</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cd "$DIR"/..</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-fi</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-if [ ! -e "./covtobed" ]; then</span></span>
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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="diff"><span class="gd" style="color: #000; background-color: #fdd;">- REMOVE=1</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- echo "WARNING:"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- echo "Binary not found: tring to use pre-compiled...";</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if [ `uname` == 'Darwin' ]; then</span></span>
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<td class="diff-line-num new new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- echo " - Copying macOS binary" || echo " ERROR: pre-compiled binary not working"</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cp ./binaries/covtobed_mac ./covtobed</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- covtobed --version</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- else</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- echo " - Trying Ubuntu binary"</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cp ./binaries/covtobed ./covtobed</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- covtobed --version || echo " ERROR: pre-compiled binary not working"</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fi</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-fi</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> </span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-./covtobed --version</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+covtobed --version</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> </span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> set -eou pipefail</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> # Compilation success, checking that --version emits the expected "progname" string</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> echo -n " - Compiled binary prints version: "</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-if [ $(./covtobed --version | grep covtobed | wc -l ) -eq "1" ];</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if [ $(covtobed --version | grep covtobed | wc -l ) -eq "1" ];</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> then</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> echo PASS 1</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> fi</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> </span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> # Testing that -m MIN produces an output, and it fits the expectation for demo.bam (n. lines)</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> echo -n " - Minimum coverage, expected BED lines check: "</span>
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<td class="diff-line-num new new_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-if [ $(./covtobed -m 15 test/demo.bam | wc -l) -eq "12" ];</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if [ $(covtobed -m 15 /usr/share/doc/covtobed-examples/examples/demo.bam | wc -l) -eq "12" ];</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> then</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> echo PASS 2</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> else</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="p">@@ -50,7 +30,7 @@</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> </span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> # Checking thath --physical-coverage will work, and it fits the expected number of lines</span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> echo -n " - Physical coverage, expected BED lines check: "</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-if [ $(./covtobed --physical-coverage test/mp.bam | wc -l) -eq "136" ];</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if [ $(covtobed --physical-coverage /usr/share/doc/covtobed-examples/examples/mp.bam | wc -l) -eq "136" ];</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> then</span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> echo PASS 3</span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> else</span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="p">@@ -60,7 +40,7 @@</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"> </span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> # Checking stranded output: it should produce content in the fifth column of the bed file</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> echo -n " - Stranded output, testing column #5: "</span>
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<td class="diff-line-num new new_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-if [ $(./covtobed --out test/demo.bam | cut -f 5 | sort -u | wc -l) -eq "10" ];</span></span>
</pre>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if [ $(covtobed --out /usr/share/doc/covtobed-examples/examples/demo.bam | cut -f 5 | sort -u | wc -l) -eq "10" ];</span></span>
</pre>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> then</span>
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<td class="diff-line-num new new_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"> echo PASS 4</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"> else</span>
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<td class="diff-line-num new new_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="p">@@ -70,7 +50,7 @@</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> # Checking the "counts" output (counting the lines containing a ">")</span>
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<td class="diff-line-num new new_line" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"> echo -n " - Testing 'counts' format (printed headers): "</span>
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<td class="diff-line-num new new_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-if [ $(./covtobed --format counts test/demo.bam | grep '>' | wc -l) -eq "2" ];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if [ $(covtobed --format counts /usr/share/doc/covtobed-examples/examples/demo.bam | grep '>' | wc -l) -eq "2" ];</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"> then</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"> echo PASS 5</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"> else</span>
</pre>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="p">@@ -78,7 +58,7 @@</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"> exit 1</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"> fi</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"> echo -n " - Testing 'counts' format (printed lines): "</span>
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<td class="diff-line-num new new_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-if [ $(./covtobed --format counts test/demo.bam | grep -v '>' | wc -l) -eq "202" ];</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if [ $(covtobed --format counts /usr/share/doc/covtobed-examples/examples/demo.bam | grep -v '>' | wc -l) -eq "202" ];</span></span>
</pre>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"> then</span>
</pre>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"> echo PASS 6</span>
</pre>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"> else</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"><span class="p">@@ -88,8 +68,8 @@</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"> # Checking BED output with reference output file</span>
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<td class="diff-line-num new new_line" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"> echo -n " - Checking identity of BED output with pre-calculated: "</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-./covtobed test/demo.bam > test/output.test</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-if [ $(diff test/output.test test/output.bed | wc -l) -eq "0" ];</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+covtobed /usr/share/doc/covtobed-examples/examples/demo.bam > output.test</span></span>
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<td class="diff-line-num new new_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if [ $(diff output.test /usr/share/doc/covtobed-examples/examples/output.bed | wc -l) -eq "0" ];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"> then</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"> echo PASS 7</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"> rm test/output.test</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"><span class="p">@@ -100,8 +80,8 @@</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"> </span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"> ## Synthetic BAM test</span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"> echo -n " - Checking computed coverage for a synthetic BAM file: "</span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-./covtobed -m 1 test/mock.bam > test/output.test</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-if [ $(diff test/output.test test/mock.bed | wc -l) -eq "0" ];</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+covtobed -m 1 /usr/share/doc/covtobed-examples/examples/mock.bam > output.test</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if [ $(diff output.test /usr/share/doc/covtobed-examples/examples/mock.bed | wc -l) -eq "0" ];</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"> then</span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"> echo PASS 8</span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"> rm test/output.test</span>
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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="diff"><span class="p">@@ -112,23 +92,23 @@</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"> </span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"> ## Filter non valid alignments</span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"> echo -n " - Checking filtering of invalid alignments: "</span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-if [ $(./covtobed -m 1 -d test/filtered.bam | wc -l) -eq "2" ] ; then</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if [ $(covtobed -m 1 -d /usr/share/doc/covtobed-examples/examples/filtered.bam | wc -l) -eq "2" ] ; then</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"> echo -n "PASS 9,"</span>
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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="diff"> else</span>
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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="diff"> echo FAIL</span>
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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="diff"> exit 1</span>
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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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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"> fi</span>
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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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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-if [ $(./covtobed -m 1 test/filtered.bam | wc -l) -eq "6" ] ; then</span></span>
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<td class="diff-line-num new new_line" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if [ $(covtobed -m 1 /usr/share/doc/covtobed-examples/examples/filtered.bam | wc -l) -eq "6" ] ; then</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"> echo 10</span>
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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
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"> else</span>
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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
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- echo "FAIL: $(./covtobed -m 1 -d test/filtered.bam | wc -l)"</span></span>
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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="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ echo "FAIL: $(covtobed -m 1 -d /usr/share/doc/covtobed-examples/examples/filtered.bam | wc -l)"</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"> exit 1</span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"> fi</span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"> </span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"> # A synthetic BAM containing reference name {n}X that should only print one reagion </span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"> # covered exactly {n}X times</span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"> echo " - Checking artificial coverage values:"</span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-./covtobed test/test_cov.bam -m 1 |cut -f 1,4| while read LINE;</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+covtobed /usr/share/doc/covtobed-examples/examples/test_cov.bam -m 1 |cut -f 1,4| while read LINE;</span></span>
</pre>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"> do</span>
</pre>
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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="diff"> echo "$LINE" | perl -ne '($exp, $cov)=split /\s+/, $_; if ("$exp" ne "${cov}X") {</span>
</pre>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"> die "$exp != $cov\n";</span>
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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="diff"><span class="p">@@ -137,7 +117,3 @@</span></span>
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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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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"> }'</span>
</pre>
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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
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"> done</span>
</pre>
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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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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"> echo "ALL TESTS: PASSED"</span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-if [[ $REMOVE -eq 1 ]]; then</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- rm ./covtobed</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-fi</span></span></pre>
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