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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>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/covtobed/-/commit/cc06efa5d2cb079d35e24bd455bd2cdddb6ba8bb">cc06efa5</a></strong>
<div>
<span>by Shayan Doust</span>
<i>at 2020-06-04T16:46:29+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Test should remove output.test not test/output.test
</pre>
</li>
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<h4>1 changed file:</h4>
<ul>
<li class="file-stats">
<a href="#a53adf029254e0148bed48d71f6702649066310d">
debian/patches/test_use_system_installed_binary.patch
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="a53adf029254e0148bed48d71f6702649066310d">
<a href="https://salsa.debian.org/med-team/covtobed/-/commit/cc06efa5d2cb079d35e24bd455bd2cdddb6ba8bb#a53adf029254e0148bed48d71f6702649066310d"><strong>debian/patches/test_use_system_installed_binary.patch</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="84" 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">@@ -84,7 +84,7 @@ Last-Update: 2020-06-04</td>
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84
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84
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="diff"> then</span>
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85
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="diff"> echo PASS 6</span>
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86
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86
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="diff"> else</span>
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87
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="diff"><span class="p">@@ -88,<span class="idiff left right">8 +68,8</span> @@</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"><span class="p">@@ -88,<span class="idiff left right">11 +68,11</span> @@</span></span>
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88
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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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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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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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="94" 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="94" 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">@@ -94,8 +94,12 @@ Last-Update: 2020-06-04</td>
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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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<pre style="margin: 0;"> <span id="LC95" class="line" lang="diff"> then</span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="diff"> echo PASS 7</span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="diff"> rm test/output.test</span>
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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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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- rm test/output.test</span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ rm output.test</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"> else</span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"> echo FAIL</span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"> exit 1</span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"><span class="p">@@ -100,11 +80,11 @@</span></span>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="diff"> ## Synthetic BAM test</span>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="diff"> echo -n " - Checking computed coverage for a synthetic BAM file: "</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="105" 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="109" 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">@@ -105,7 +109,11 @@ Last-Update: 2020-06-04</td>
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105
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109
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<pre style="margin: 0;"> <span id="LC109" 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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<td class="diff-line-num old_line" data-linenumber="106" 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">
106
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110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="diff"> then</span>
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<td class="diff-line-num old_line" data-linenumber="107" 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">
107
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111
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<pre style="margin: 0;"> <span id="LC111" 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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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- rm test/output.test</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ rm output.test</span></span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"> else</span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"> echo FAIL</span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"> exit 1</span>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="diff"><span class="p">@@ -112,23 +92,23 @@</span></span>
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="diff"> ## Filter non valid alignments</span>
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