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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/sambamba">Debian Med / sambamba</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/sambamba/commit/22dc4a7940dc5de9eada1184d972cdcab89ba973">22dc4a79</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-04T08:06:06Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.6.8</pre>
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<h4>21 changed files:</h4>
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<li class="file-stats">
<a href="#7445606fbf8f3683cd42bdc54b05d7a0bc2dfc44">
.gitmodules
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<li class="file-stats">
<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
.travis.yml
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<li class="file-stats">
<a href="#b2270542d41297db1ee0d12698e609ea3ec25ce7">
INSTALL.md
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<li class="file-stats">
<a href="#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
Makefile
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<li class="file-stats">
<a href="#544fe3dec8c6dbfa9ec37b21822a8554798b2423">
Makefile.guix
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<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<li class="file-stats">
<a href="#6f8a88f369eae9b2f3ece90d1ba6366a16f25f9c">
RELEASE-NOTES.md
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<a href="#ee1c3381ed1e67657ca0073d77279ffa7aed97fa">
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+
contrib/shunit2-2.0.3/CHANGES-2.0.txt
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contrib/shunit2-2.0.3/LGPL-2.1
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contrib/shunit2-2.0.3/README.txt
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contrib/shunit2-2.0.3/contributors.txt
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contrib/shunit2-2.0.3/shunit2
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<a href="#fa4f48178d1a329d4f6de31408787bc1c9c0ab80">
cram/htslib.d
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<li class="file-stats">
<a href="#a96f9198894d01fd66b763d98c3607cb6966a401">
gen_ldc_version_info.py
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<a href="#da8c3529949805abe1b73685532823c3fb63b1a9">
run_tests.sh
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<a href="#3b3ae0b610f6ae26ed107e183c7ee027e957b1ed">
sambamba/main.d
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<a href="#b888d326ed4b8a8c518a69a5de5f0ae9bc642ef9">
sambamba/markdup.d
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<a href="#a2dfc645061c612393c9e78b784b01f62f7a0e42">
test/benchmark/stats.org
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<a href="#076a163a9686c6ad68d6256408877818d28a30e8">
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test/issue_356.sam
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<a href="#3708ce0a178d356e1f2b2d1b351aeb02556a5a7a">
test/test_suite.sh
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<a href="#f3336b1428b648374b0d29c18036eee01ed71db1">
utils/version_.d
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<h4>Changes:</h4>
<li id="7445606fbf8f3683cd42bdc54b05d7a0bc2dfc44">
<a href="https://salsa.debian.org/med-team/sambamba/commit/22dc4a7940dc5de9eada1184d972cdcab89ba973#7445606fbf8f3683cd42bdc54b05d7a0bc2dfc44"><strong>.gitmodules</strong></a>
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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="LC1" class="line" lang="plaintext">[submodule "htslib"]</span>
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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"> path = htslib</span>
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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"> url = https://github.com/lomereiter/htslib.git</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">[submodule "undeaD"]</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> path = undeaD</span>
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<td class="diff-line-num old old_line" data-linenumber="6" 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="LC6" class="line" lang="plaintext"> url = https://github.com/dlang/undeaD</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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<td class="diff-line-num new_line old" data-linenumber="4" 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="plaintext">[submodule "BioD"]</span>
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<td class="diff-line-num old old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="diff-line-num new_line old" data-linenumber="4" 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="LC8" class="line" lang="plaintext"> path = BioD</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="plaintext"> url = https://github.com/biod/BioD.git</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">[submodule "lz4"]</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> path = lz4</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> url = https://github.com/lz4/lz4.git</span>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">[submodule "BioD"]</span>
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> path = BioD</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">
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> url = https://github.com/biod/BioD.git</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">[submodule "undeaD"]</span>
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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"> path = undeaD</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> url = https://github.com/biod/undeaD.git</span></pre>
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<li id="dea01dd89a3b602828e630677fde5d77c06441c8">
<a href="https://salsa.debian.org/med-team/sambamba/commit/22dc4a7940dc5de9eada1184d972cdcab89ba973#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</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">@@ -8,15 +8,8 @@ matrix:</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="yaml"> <span class="na" style="color: teal;">include</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: teal;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">linux</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="yaml"> <span class="na" style="color: teal;">compiler</span><span class="pi">:</span> <span class="s" style="color: #d14;">gcc</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="yaml"> <span class="na" style="color: teal;">addons</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="yaml"> <span class="na" style="color: teal;">apt</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="yaml"> <span class="na" style="color: teal;">packages</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># Our dev environment is a more recent GNU C++</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># note that Debian liblz4-dev no longer supports LZ4 frames</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># - liblz4-dev</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">shunit2</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: teal;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">osx</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="yaml"> <span class="na" style="color: teal;">compiler</span><span class="pi">:</span> <span class="s" style="color: #d14;">clang</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="yaml"><span class="na" style="color: teal;">script</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">make</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># - make test - disable tests because shunit2 we use is older</span></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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<pre style="margin: 0;">+<span id="LC15" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">make check</span></span></pre>
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<li id="b2270542d41297db1ee0d12698e609ea3ec25ce7">
<a href="https://salsa.debian.org/med-team/sambamba/commit/22dc4a7940dc5de9eada1184d972cdcab89ba973#b2270542d41297db1ee0d12698e609ea3ec25ce7"><strong>INSTALL.md</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,10 +2,27 @@</td>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Sambamba dependencies</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="markdown"></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="markdown"><span class="p">*</span> D compiler</span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="markdown"><span class="p">*</span> <span class="idiff left right">gcc tool chain</span></span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="markdown"><span class="p">*</span> <span class="idiff left right">BioD</span></span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="markdown"><span class="p">*</span> htslib</span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="markdown"><span class="p">*</span> undeaD</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"><span class="p">*</span> D compiler<span class="idiff left right"> (ldc)</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"><span class="p">*</span> <span class="idiff left right">BioD (git submodule)</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown"><span class="p">*</span> <span class="idiff left right">gcc tool chain (for htslib and lz4)</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown"><span class="p">*</span> htslib<span class="idiff left right"> (git submodule)</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown"><span class="p">*</span> undeaD<span class="idiff left right"> (git submodule)</span></span>
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10
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="markdown"><span class="p">*</span> libz</span>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="markdown"><span class="p">*</span> liblz4</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown"></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Install Sambamba from source</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="markdown">After checking out the source from github with git submodules is is</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="markdown">possibleto install the build tools with GNU Guix</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="markdown"><span class="sb" style="color: #d14;"> guix package -i gcc gdb bash ld-wrapper ldc which python2 git</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="markdown">Even better, with Guix, you can create a light-weight container in the source tree</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="markdown">and run our development setup</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="markdown"><span class="sb" style="color: #d14;"> guix environment -C guix --ad-hoc gcc gdb bash ld-wrapper ldc which python git</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="markdown"><span class="sb" style="color: #d14;"> make clean</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="markdown"><span class="sb" style="color: #d14;"> make -j 4</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="markdown"><span class="sb" style="color: #d14;"> make check</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="markdown">this way all dependencies are isolated.</span></pre>
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<a href="https://salsa.debian.org/med-team/sambamba/commit/22dc4a7940dc5de9eada1184d972cdcab89ba973#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c"><strong>Makefile</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># This is a minimalistic make file to build sambamba with ldc2 as per instructions on</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># https://github.com/biod/sambamba#compiling-sambamba</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Targets (64-bit):</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Linux</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># OSX</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Typical usage:</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># <span class="idiff left right"> make LIBRARY_PATH=~/opt/ldc2-1.7.0</span>-linux-x86_64/lib debug|profile|release|static</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># <span class="idiff left right">make LIBRARY_PATH=~/opt/ldc2-$ver</span>-linux-x86_64/lib debug|profile|release|static</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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<td class="diff-line-num new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Static release with optimization (for releases):</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># make LIBRARY_PATH=~/opt/ldc2-<span class="idiff left right">1.7.0</span>-linux-x86_64/lib pgo-static</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># make LIBRARY_PATH=~/opt/ldc2-<span class="idiff left right">$ver</span>-linux-x86_64/lib pgo-static</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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<td class="diff-line-num 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">
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Debug version</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># make LIBRARY_PATH=~/opt/ldc2-1.7.0-linux-x86_64/lib debug</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># make LIBRARY_PATH=~/opt/ldc2-$ver-linux-x86_64/lib debug</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="make"></span>
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16
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="make"><span class="nv" style="color: teal;">D_COMPILER</span><span class="o" style="font-weight: 600;">=</span>ldc2</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="make"></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="make"><span class="nv" style="color: teal;">UNAME_S</span> <span class="o" style="font-weight: 600;">:=</span> <span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">shell</span> <span class="nb" style="color: #0086b3;">uname</span> <span class="nt" style="color: navy;">-s</span><span class="nv" style="color: teal;">)</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">ifeq</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">($(UNAME_S),Darwin)</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="make"> <span class="nv" style="color: teal;">SYS</span> <span class="o" style="font-weight: 600;">=</span> OSX</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">else</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="make"> <span class="nv" style="color: teal;">SYS</span> <span class="o" style="font-weight: 600;">=</span> LINUX</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="make"> <span class="nv" style="color: teal;">LINK_OBJ</span> <span class="o" style="font-weight: 600;">=</span> utils/ldc_version_info_.o</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">endif</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="make"></span>
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17
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="make"><span class="nv" style="color: teal;">DFLAGS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: navy;">-wi</span> <span class="nt" style="color: navy;">-I</span><span class="nb" style="color: #0086b3;">.</span> <span class="nt" style="color: navy;">-IBioD</span> <span class="nt" style="color: navy;">-IundeaD</span>/src <span class="nt" style="color: navy;">-g</span></span>
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18
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="make"><span class="nv" style="color: teal;">DLIBS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$(LIBRARY_PATH)</span>/libphobos2-ldc.a <span class="nv" style="color: teal;">$(LIBRARY_PATH)</span>/libdruntime-ldc.a</span>
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20
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="make"><span class="nv" style="color: teal;">DLIBS_DEBUG</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$(LIBRARY_PATH)</span>/libphobos2-ldc-debug.a <span class="nv" style="color: teal;">$(LIBRARY_PATH)</span>/libdruntime-ldc-debug.a</span>
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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="make"><span class="nv" style="color: teal;">LIBS</span> <span class="o" style="font-weight: 600;">=</span> htslib/libhts.a lz4/lib/liblz4.a <span class="nt" style="color: navy;">-L-L</span><span class="nv" style="color: teal;">$(LIBRARY_PATH)</span> <span class="nt" style="color: navy;">-L-l<span class="idiff left">rt</span></span><span class="idiff"> </span><span class="nt" style="color: navy;"><span class="idiff right">-L-l</span>pthread</span> <span class="nt" style="color: navy;">-L-lm</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="make"><span class="nv" style="color: teal;">LIBS</span> <span class="o" style="font-weight: 600;">=</span> htslib/libhts.a lz4/lib/liblz4.a <span class="nt" style="color: navy;">-L-L</span><span class="nv" style="color: teal;">$(LIBRARY_PATH)</span> <span class="nt" style="color: navy;">-L-lpthread</span> <span class="nt" style="color: navy;">-L-lm</span></span>
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22
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37
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="make"><span class="nv" style="color: teal;">LIBS_STATIC</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$(LIBRARY_PATH)</span>/libc.a <span class="nv" style="color: teal;">$(DLIBS)</span> htslib/libhts.a <span class="nv" style="color: teal;">$(LIBRARY_PATH)</span>/liblz4.a</span>
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23
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38
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="make"><span class="nv" style="color: teal;">SRC</span> <span class="o" style="font-weight: 600;">=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>wildcard main.d utils/<span class="k" style="font-weight: 600;">*</span>.d thirdparty/<span class="k" style="font-weight: 600;">*</span>.d cram/<span class="k" style="font-weight: 600;">*</span>.d<span class="o" style="font-weight: 600;">)</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>wildcard undeaD/src/undead/<span class="k" style="font-weight: 600;">*</span>.d<span class="o" style="font-weight: 600;">)</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>wildcard BioD/bio/<span class="k" style="font-weight: 600;">*</span>/<span class="k" style="font-weight: 600;">*</span>.d BioD/bio/<span class="k" style="font-weight: 600;">*</span>/<span class="k" style="font-weight: 600;">*</span>/<span class="k" style="font-weight: 600;">*</span>.d BioD/bio2/<span class="k" style="font-weight: 600;">*</span>.d BioD/bio2/<span class="k" style="font-weight: 600;">*</span>/<span class="k" style="font-weight: 600;">*</span>.d<span class="o" style="font-weight: 600;">)</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>wildcard sambamba/<span class="k" style="font-weight: 600;">*</span>.d sambamba/<span class="k" style="font-weight: 600;">*</span>/<span class="k" style="font-weight: 600;">*</span>.d sambamba/<span class="k" style="font-weight: 600;">*</span>/<span class="k" style="font-weight: 600;">*</span>/<span class="k" style="font-weight: 600;">*</span>.d<span class="o" style="font-weight: 600;">)</span></span>
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24
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39
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="make"><span class="nv" style="color: teal;">OBJ</span> <span class="o" style="font-weight: 600;">=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>SRC:.d<span class="o" style="font-weight: 600;">=</span>.o<span class="o" style="font-weight: 600;">)</span> utils/ldc_version_info_.o</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -49,7 +64,7 @@ htslib-static:</td>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="make"> <span class="nb" style="color: #0086b3;">cd </span>htslib <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: teal;">$(MAKE)</span></span>
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50
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="make"></span>
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51
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66
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="make"><span class="nl">ldc-version-info</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="make"> ./gen_ldc_version_info.py <span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">shell</span> which ldmd2<span class="nv" style="color: teal;">)</span> <span class="o" style="font-weight: 600;">></span> utils/ldc_version_info_.d</span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="make"> <span class="idiff left right">python3 </span>./gen_ldc_version_info.py <span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">shell</span> which ldmd2<span class="nv" style="color: teal;">)</span> <span class="o" style="font-weight: 600;">></span> utils/ldc_version_info_.d</span>
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53
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="make"> <span class="nb" style="color: #0086b3;">cat </span>utils/ldc_version_info_.d</span>
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54
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69
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="make"><span class="nl">utils/ldc_version_info_.o</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">ldc-version-info</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="78" 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="93" 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">@@ -78,7 +93,7 @@ singleobj:</td>
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78
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># ---- Link step</span></span>
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79
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="make"><span class="nl">$(OUT)</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">build-setup singleobj utils/ldc_version_info_.o</span></span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>info linking...<span class="o" style="font-weight: 600;">)</span></span>
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81
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="make"> <span class="nv" style="color: teal;">$(D_COMPILER)</span> <span class="nv" style="color: teal;">$(DFLAGS)</span> <span class="nt" style="color: navy;">-of</span><span class="o" style="font-weight: 600;">=</span>bin/sambamba bin/sambamba.o <span class="idiff left right">utils/ldc_version_info_.o</span> <span class="nv" style="color: teal;">$(LIBS)</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="make"> <span class="nv" style="color: teal;">$(D_COMPILER)</span> <span class="nv" style="color: teal;">$(DFLAGS)</span> <span class="nt" style="color: navy;">-of</span><span class="o" style="font-weight: 600;">=</span>bin/sambamba bin/sambamba.o <span class="nv" style="color: teal;"><span class="idiff left right">$(LINK_OBJ)</span></span> <span class="nv" style="color: teal;">$(LIBS)</span></span>
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82
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="make"></span>
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83
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="make"><span class="nl">test</span><span class="o" style="font-weight: 600;">:</span></span>
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84
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="make"> ./run_tests.sh</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -97,7 +112,7 @@ install:</td>
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97
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="make"> <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: navy;">-m</span> 0755 bin/sambamba <span class="nv" style="color: teal;">$(prefix)</span>/bin</span>
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98
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113
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="make"></span>
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99
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114
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="make"><span class="nl">clean</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">clean-d</span></span>
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100
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="make"> <span class="nb" style="color: #0086b3;">cd </span>htslib <span class="p">;</span> <span class="idiff left right">make</span> clean</span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="make"> <span class="nb" style="color: #0086b3;">cd </span>htslib <span class="p">;</span> <span class="nv" style="color: teal;"><span class="idiff left right">$(MAKE)</span></span> clean</span>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: navy;">-f</span> profile.data</span>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: navy;">-f</span> profile.raw</span>
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="make"></span>
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<a href="https://salsa.debian.org/med-team/sambamba/commit/22dc4a7940dc5de9eada1184d972cdcab89ba973#544fe3dec8c6dbfa9ec37b21822a8554798b2423"><strong>Makefile.guix</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># GNU Guix makefile. GNU Guix is the package manager for GNU and we<span class="idiff left right"> use it for</span></span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># <span class="idiff left right">sambamba development and deployment. Normally use the standard Makefil</span>e</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># <span class="idiff left right">instead</span>.</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># GNU Guix makefile. GNU Guix is the package manager for GNU and we</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># <span class="idiff left right">use it for sambamba development and deployment. Normally use th</span>e</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># <span class="idiff left right">standard Makefile instead because it compiles into a singleobj</span>.</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># To build sambamba on GNU Guix:</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># make -f Makefile.guix</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># make -f Makefile.guix<span class="idiff left right"> GUIX=~/opt/sambamba-dev-env</span></span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># run with</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">#</span></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">@@ -18,7 +18,10 @@</td>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># The following two are modified by the Guix package:</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="make"><span class="nv" style="color: teal;">D_COMPILER</span><span class="o" style="font-weight: 600;">=</span>ldc2</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="make"><span class="nv" style="color: teal;">LDC_LIB_PATH</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">$(HOME)</span>/.guix-profile/lib</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">ifndef</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">GUIX</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="make"> <span class="nv" style="color: teal;">GUIX</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">$(HOME)</span>/.guix-profile</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">endif</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="make"><span class="nv" style="color: teal;">LDC_LIB_PATH</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">$(GUIX)</span>/lib</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="make"><span class="nv" style="color: teal;">UNDEAD_PATH</span><span class="o" style="font-weight: 600;">=</span>../undeaD/src</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="make"><span class="nv" style="color: teal;">BIOD_PATH</span><span class="o" style="font-weight: 600;">=</span>../BioD</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">@@ -31,7 +34,7 @@ RPATH = -L--rpath=$(dir $(realpath $(LDC_LIB_PATH)/libz.so)):$(dir $(realpath $</td>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="make"><span class="nv" style="color: teal;">LIBS</span> <span class="o" style="font-weight: 600;">=</span> htslib/libhts.a <span class="nt" style="color: navy;">-L-L</span><span class="nv" style="color: teal;">$(LDC_LIB_PATH)</span> <span class="nt" style="color: navy;">-L-lrt</span> <span class="nt" style="color: navy;">-L-lpthread</span> <span class="nt" style="color: navy;">-L-lm</span> <span class="nt" style="color: navy;">-L-lz</span> <span class="nt" style="color: navy;">-L-llz4</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># LIBS = htslib/libhts.a -L-lrt -L-lpthread -L-lm -L-lz -L-llz4</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="make"><span class="nv" style="color: teal;">LIBS_STATIC</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$(DLIBS)</span> htslib/libhts.a <span class="nv" style="color: teal;">$(LDC_LIB_PATH)</span>/liblz4.a</span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="make"><span class="nv" style="color: teal;">SRC</span> <span class="o" style="font-weight: 600;"><span class="idiff left">=</span></span><span class="idiff"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">$</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="idiff">wildcard utils/</span><span class="k" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff">.d thirdparty/</span><span class="k" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff">.d cram/</span><span class="k" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff">.d</span><span class="o" style="font-weight: 600;"><span class="idiff">)</span></span><span class="idiff"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">$</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="idiff">wildcard </span><span class="nv" style="color: teal;"><span class="idiff">$(UNDEAD_PATH)</span></span><span class="idiff">/undead/</span><span class="k" style="font-weight: 600;"><span class="idiff">**</span></span><span class="idiff">/</span><span class="k" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff">.d</span><span class="o" style="font-weight: 600;"><span class="idiff">)</span></span><span class="idiff"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">$</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="idiff">wildcard </span><span class="nv" style="color: teal;"><span class="idiff">$(UNDEAD_PATH)</span></span><span class="idiff">/undead/</span><span class="k" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff">.d</span><span class="o" style="font-weight: 600;"><span class="idiff">)</span></span><span class="idiff"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">$</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="idiff">wildcard </span><span class="nv" style="color: teal;"><span class="idiff">$(BIOD_PATH)</span></span><span class="idiff">/bio/</span><span class="k" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff">/</span><span class="k" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff">.d </span><span class="nv" style="color: teal;"><span class="idiff">$(BIOD_PATH)</span></span><span class="idiff">/bio/</span><span class="k" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff">/</span><span class="k" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff">/</span><span class="k" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff">.d</span><span class="o" style="font-weight: 600;"><span class="idiff">)</span></span><span class="idiff"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">$</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="idiff">wildcard sambamba/</span><span class="k" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff">.d sambamba/</span><span class="k" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff">/</span><span class="k" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff">.d sambamba/</span><span class="k" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff">/</span><span class="k" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff">/</span><span class="k" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff">.d</span><span class="o" style="font-weight: 600;"><span class="idiff">)</span></span><span class="idiff right"> utils/ldc_version_info_.d</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="make"><span class="nv" style="color: teal;">SRC</span> <span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">$</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="idiff">wildcard main.d utils/</span><span class="k" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff">.d thirdparty/</span><span class="k" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff">.d cram/</span><span class="k" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff">.d</span><span class="o" style="font-weight: 600;"><span class="idiff">)</span></span><span class="idiff"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">$</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="idiff">wildcard undeaD/src/undead/</span><span class="k" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff">.d undeaD/src/undead/</span><span class="k" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff">/</span><span class="k" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff">.d</span><span class="o" style="font-weight: 600;"><span class="idiff">)</span></span><span class="idiff"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">$</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="idiff">wildcard BioD/bio/</span><span class="k" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff">/</span><span class="k" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff">.d BioD/bio/</span><span class="k" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff">/</span><span class="k" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff">/</span><span class="k" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff">.d BioD/bio2/</span><span class="k" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff">.d BioD/bio2/</span><span class="k" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff">/</span><span class="k" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff">.d</span><span class="o" style="font-weight: 600;"><span class="idiff">)</span></span><span class="idiff"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">$</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="idiff">wildcard sambamba/</span><span class="k" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff">.d sambamba/</span><span class="k" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff">/</span><span class="k" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff">.d sambamba/</span><span class="k" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff">/</span><span class="k" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff">/</span><span class="k" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff">.d</span><span class="o" style="font-weight: 600;"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="make"><span class="nv" style="color: teal;">OBJ</span> <span class="o" style="font-weight: 600;">=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>SRC:.d<span class="o" style="font-weight: 600;">=</span>.o<span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="make"><span class="nv" style="color: teal;">OUT</span> <span class="o" style="font-weight: 600;">=</span> bin/sambamba</span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="make"></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">@@ -2,15 +2,36 @@</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="markdown"><span class="gh" style="color: #999;"># sambamba</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="markdown"></span>
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5
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<td class="diff-line-num new_line old" data-linenumber="5" 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="LC5" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Table of Contents</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">Table of Contents</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">=================</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: teal;">sambamba</span><span class="p">](</span><span class="sx" style="color: #d14;">#sambamba</span><span class="p">)</span></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="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: teal;">Table of Contents</span><span class="p">](</span><span class="sx" style="color: #d14;">#table-of-contents</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: teal;">Introduction</span><span class="p">](</span><span class="sx" style="color: #d14;">#introduction</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: teal;">Binary installation</span><span class="p">](</span><span class="sx" style="color: #d14;">#binary-installation</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="6" style="width: 35px; color: rgba(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="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: teal;">Install stable release</span><span class="p">](</span><span class="sx" style="color: #d14;">#install-stable-release</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: teal;">Bioconda install</span><span class="p">](</span><span class="sx" style="color: #d14;">#bioconda-install</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="6" style="width: 35px; color: rgba(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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<pre style="margin: 0;">+<span id="LC14" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: teal;">GNU Guix install</span><span class="p">](</span><span class="sx" style="color: #d14;">#gnu-guix-install</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: teal;">Debian GNU/Linux install</span><span class="p">](</span><span class="sx" style="color: #d14;">#debian-gnulinux-install</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: teal;">Homebrew install</span><span class="p">](</span><span class="sx" style="color: #d14;">#homebrew-install</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: teal;">Getting help</span><span class="p">](</span><span class="sx" style="color: #d14;">#getting-help</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="6" style="width: 35px; color: rgba(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="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: teal;">Reporting a sambamba bug or issue</span><span class="p">](</span><span class="sx" style="color: #d14;">#reporting-a-sambamba-bug-or-issue</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: teal;">Check list:</span><span class="p">](</span><span class="sx" style="color: #d14;">#check-list</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: teal;">Code of conduct</span><span class="p">](</span><span class="sx" style="color: #d14;">#code-of-conduct</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: teal;">Compiling Sambamba</span><span class="p">](</span><span class="sx" style="color: #d14;">#compiling-sambamba</span><span class="p">)</span></span>
</pre>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: teal;">Compilation dependencies</span><span class="p">](</span><span class="sx" style="color: #d14;">#compilation-dependencies</span><span class="p">)</span></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="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: teal;">Compiling for Linux</span><span class="p">](</span><span class="sx" style="color: #d14;">#compiling-for-linux</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: teal;">GNU Guix</span><span class="p">](</span><span class="sx" style="color: #d14;">#gnu-guix</span><span class="p">)</span></span>
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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="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: teal;">Compiling for Mac OS X</span><span class="p">](</span><span class="sx" style="color: #d14;">#compiling-for-mac-os-x</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: teal;">Development</span><span class="p">](</span><span class="sx" style="color: #d14;">#development</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: teal;">Debugging and troubleshooting</span><span class="p">](</span><span class="sx" style="color: #d14;">#debugging-and-troubleshooting</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: teal;">Segfaults on certain Intel Xeons</span><span class="p">](</span><span class="sx" style="color: #d14;">#segfaults-on-certain-intel-xeons</span><span class="p">)</span></span>
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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="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: teal;">Dump core</span><span class="p">](</span><span class="sx" style="color: #d14;">#dump-core</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: teal;">Use catchsegv</span><span class="p">](</span><span class="sx" style="color: #d14;">#use-catchsegv</span><span class="p">)</span></span>
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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="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: teal;">Using gdb</span><span class="p">](</span><span class="sx" style="color: #d14;">#using-gdb</span><span class="p">)</span></span>
</pre>
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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="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: teal;">License</span><span class="p">](</span><span class="sx" style="color: #d14;">#license</span><span class="p">)</span></span>
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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="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: teal;">Credit</span><span class="p">](</span><span class="sx" style="color: #d14;">#credit</span><span class="p">)</span></span>
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6
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<td class="diff-line-num new_line" data-linenumber="34" 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">
34
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="markdown"></span>
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7
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<td class="diff-line-num new_line old" data-linenumber="35" 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="markdown"><span class="p">-</span> <span class="p">[</span><span class="nv" style="color: teal;">Introduction</span><span class="p">](</span><span class="sx" style="color: #d14;">#intro</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="8" 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">
8
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<td class="diff-line-num new_line old" data-linenumber="35" 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="LC8" class="line" lang="markdown"><span class="p">-</span> <span class="p">[</span><span class="nv" style="color: teal;">Binary installation</span><span class="p">](</span><span class="sx" style="color: #d14;">#install</span><span class="p">)</span></span>
</pre>
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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">
9
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<td class="diff-line-num new_line old" data-linenumber="35" 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="markdown"><span class="p">-</span> <span class="p">[</span><span class="nv" style="color: teal;">Getting help</span><span class="p">](</span><span class="sx" style="color: #d14;">#help</span><span class="p">)</span></span>
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10
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<td class="diff-line-num new_line old" data-linenumber="35" 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="LC10" class="line" lang="markdown"><span class="p">-</span> <span class="p">[</span><span class="nv" style="color: teal;">Compiling</span><span class="p">](</span><span class="sx" style="color: #d14;">#compile</span><span class="p">)</span></span>
</pre>
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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">
11
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<td class="diff-line-num new_line old" data-linenumber="35" 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="markdown"><span class="p">-</span> <span class="p">[</span><span class="nv" style="color: teal;">Debugging and troubleshooting</span><span class="p">](</span><span class="sx" style="color: #d14;">#debug</span><span class="p">)</span></span>
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12
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<td class="diff-line-num new_line old" data-linenumber="35" 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="LC12" class="line" lang="markdown"><span class="p">-</span> <span class="p">[</span><span class="nv" style="color: teal;">License</span><span class="p">](</span><span class="sx" style="color: #d14;">#license</span><span class="p">)</span></span>
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13
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<td class="diff-line-num new_line old" data-linenumber="35" 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="LC13" class="line" lang="markdown"><span class="p">-</span> <span class="p">[</span><span class="nv" style="color: teal;">Credits</span><span class="p">](</span><span class="sx" style="color: #d14;">#credits</span><span class="p">)</span></span>
</pre>
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14
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35
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="markdown"></span>
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15
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36
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="markdown"><span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">name=</span><span class="s" style="color: #d14;">"intro"</span><span class="nt" style="color: navy;">></a></span></span>
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16
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="markdown"><span class="gh" style="color: #999;"># Introduction</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -33,8 +54,8 @@ configurations. Here are some comparison</td>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">metrics</span><span class="p">](</span><span class="sx" style="color: #d14;">https://public-docs.crg.es/rguigo/Data/epalumbo/sambamba_ws_report.html</span><span class="p">)</span>. For</span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="markdown">example for flagstat sambamba is 1.4x faster than samtools. For index</span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="markdown">they are similar. For Markdup almost 6x faster and for view 4x</span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="markdown">faster. For sort sambamba has been beaten<span class="idiff left right"> generally, though sambamba</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="markdown"><span class="idiff left right">is up to 2x faster on large RAM machines</span>.</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="markdown">faster. For sort sambamba has been beaten<span class="idiff left right">, though sambamba is up to 2x</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="markdown"><span class="idiff left right">faster than samtools on large RAM machines (120GB+)</span>.</span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="markdown">In addition sambamba has a few interesting features to offer, in particular</span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="markdown"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="58" 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="79" 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">@@ -58,7 +79,7 @@ Sambamba is free and open source software, licensed under GPLv2+.</td>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="markdown">See manual pages <span class="p">[</span><span class="nv" style="color: teal;">online</span><span class="p">](</span><span class="sx" style="color: #d14;">https://lomereiter.github.io/sambamba/docs/sambamba-view.html</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="markdown">to know more about what is available and how to use it.</span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="markdown">For more information on Sambamba contact the mailing list (see <span class="idiff left right">below</span>).</span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="markdown">For more information on Sambamba contact the mailing list (see <span class="p"><span class="idiff left">[</span></span><span class="nv" style="color: teal;"><span class="idiff">Getting help</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">#getting-help</span></span><span class="p"><span class="idiff right">)</span></span>).</span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="markdown"><span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">name=</span><span class="s" style="color: #d14;">"install"</span><span class="nt" style="color: navy;">></a></span></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="markdown"><span class="gh" style="color: #999;"># Binary installation</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="90" 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">@@ -69,7 +90,7 @@ are Github source and binary</td>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">releases</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/biod/sambamba/releases</span><span class="p">)</span>. Simply download</span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="markdown">the tarball, unpack it and run it. For example</span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="markdown"><span class="p">```</span><span class="nl">sh</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="markdown"><span class="p">```</span><span class="nl"><span class="idiff left right">ba</span>sh</span></span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="markdown">wget https://github.com/biod/sambamba/releases/download/v0.6.8/sambamba_v0.6.8_linux.tar.bz2</span>
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95
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">tar </span>xvjf sambamba_v0.6.8_linux.tar.bz2</span>
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75
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96
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="markdown">./sambamba_v0.6.8</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="95" 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="116" 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">@@ -95,13 +116,12 @@ A [GNU Guix package](https://www.gnu.org/software/guix/packages/s.html) for samb</td>
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95
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116
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="markdown"></span>
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96
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Debian GNU/Linux install</span></span>
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="markdown"></span>
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98
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="markdown">Debian: see <span class="idiff left right">Debian packages</span>.</span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="markdown">Debian: see <span class="p"><span class="idiff left">[</span></span><span class="nv" style="color: teal;"><span class="idiff">Debian packages</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">https://tracker.debian.org/pkg/sambamba</span></span><span class="p"><span class="idiff right">)</span></span>.</span>
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99
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120
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Homebrew install</span></span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="markdown">Users of Homebrew can also use the formula from <span class="sb" style="color: #d14;">`homebrew-science`</span>.</span>
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="markdown"></span>
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104
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="markdown"><span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">name=</span><span class="s" style="color: #d14;">"help"</span><span class="nt" style="color: navy;">></a></span></span>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="markdown"><span class="gh" style="color: #999;"># Getting help</span></span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="markdown"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="155" 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="175" 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">@@ -155,20 +175,11 @@ Note: in general there is no need to compile sambamba. You can use a</td>
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155
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="markdown">recent binary install as listed above.</span>
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156
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176
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="markdown"></span>
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157
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="markdown">The preferred method for compiling Sambamba is with the LDC compiler</span>
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158
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<td class="diff-line-num new_line old" data-linenumber="178" 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="LC158" class="line" lang="markdown">which targets LLVM.</span>
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="markdown">which targets LLVM.<span class="idiff left right"> LLVM versions 6 is faster than earlier editions.</span></span>
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159
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179
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="markdown"></span>
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160
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180
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Compilation dependencies</span></span>
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161
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181
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="markdown"></span>
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162
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="markdown"><span class="p">-</span> git (to check out the repo)</span>
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163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="markdown"><span class="p">-</span> gcc compiler 4.9 or later (for htslib)</span>
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164
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="markdown"><span class="p">-</span> D compiler 1.7.0 or later (ldc2, see below)</span>
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165
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="markdown"><span class="p">-</span> python2 (parses D-compiler header for version info)</span>
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166
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="markdown"><span class="p">-</span> zlib (library)</span>
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167
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="markdown"><span class="p">-</span> lz4 (library)</span>
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168
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="markdown"><span class="p">-</span> htslib (submodule)</span>
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169
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="markdown"><span class="p">-</span> BioD (source)</span>
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170
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="markdown"><span class="p">-</span> undeaD (source)</span>
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171
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="markdown"><span class="p">-</span> python2</span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="markdown">See <span class="p">[</span><span class="nv" style="color: teal;">INSTALL.md</span><span class="p">](</span><span class="sx" style="color: #d14;">./INSTALL.md</span><span class="p">)</span>.</span>
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172
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183
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="markdown"></span>
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173
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Compiling for Linux</span></span>
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174
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185
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="markdown"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="190" 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="201" 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">@@ -190,7 +201,7 @@ cd sambamba</td>
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="markdown">make</span>
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<td class="diff-line-num old_line" data-linenumber="191" 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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<pre style="margin: 0;"> <span id="LC202" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="193" 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">
193
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="markdown">To build a de<span class="idiff left right">bug release</span> run</span>
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="markdown">To build a de<span class="idiff left right">velopment/debug version</span> run</span>
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194
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205
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="markdown"></span>
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<td class="diff-line-num old_line" data-linenumber="195" 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">
195
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="markdown"><span class="p">```</span><span class="nl">sh</span></span>
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196
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="markdown">make clean <span class="o" style="font-weight: 600;">&&</span> make debug</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">@@ -203,6 +214,8 @@ you can run</td>
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="markdown">make check</span>
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC216" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="markdown">See also <span class="p">[</span><span class="nv" style="color: teal;">INSTALL.md</span><span class="p">](</span><span class="sx" style="color: #d14;">./INSTALL.md</span><span class="p">)</span>.</span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC219" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### GNU Guix</span></span>
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC221" class="line" lang="markdown">To build sambamba the LDC compiler is also available in GNU Guix:</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">@@ -213,15 +226,14 @@ guix package -i ldc</td>
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Compiling for Mac OS X</span></span>
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<pre style="margin: 0;"> <span id="LC228" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="markdown"><span class="idiff left right">Note: the Makefile does not work. Someone want to fix that using the</span></span>
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<pre style="margin: 0;">-<span id="LC217" class="line" lang="markdown"><span class="idiff left right">Makefile.old version? See also https://github.com/biod/sambamba/issues/338.</span></span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="markdown"><span class="idiff left">Sambamba builds on MacOS. We have a Travis </span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: teal;"><span class="idiff">integration test</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">https://travis-ci.org/pjotrp/sambamba</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> as</span></span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="markdown"><span class="idiff left right">an example. It can be something like</span></span>
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="markdown"><span class="p">```</span><span class="nl">sh</span></span>
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<pre style="margin: 0;"> <span id="LC233" class="line" lang="markdown"> brew <span class="nb" style="color: #0086b3;">install </span>ldc</span>
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<pre style="margin: 0;"> <span id="LC234" class="line" lang="markdown"> git clone <span class="nt" style="color: navy;">--recursive</span> https://github.com/biod/sambamba.git</span>
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<pre style="margin: 0;"> <span id="LC235" class="line" lang="markdown"> <span class="nb" style="color: #0086b3;">cd </span>sambamba</span>
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<pre style="margin: 0;">-<span id="LC223" class="line" lang="markdown"> git clone https://github.com/dlang/undeaD</span>
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<pre style="margin: 0;">-<span id="LC224" class="line" lang="markdown"> make sambamba-ldmd2-64</span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="markdown"> make</span>
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<pre style="margin: 0;"> <span id="LC237" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC238" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC239" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Development</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="232" 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="244" 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">@@ -232,6 +244,7 @@ documentation can be found in the source code and the [development</td>
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="markdown">documentation](https://github.com/biod/sambamba-dev-docs).</span>
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<td class="diff-line-num old_line" data-linenumber="233" 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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<pre style="margin: 0;"> <span id="LC245" class="line" lang="markdown"></span>
</pre>
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="markdown"><span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">name=</span><span class="s" style="color: #d14;">"debug"</span><span class="nt" style="color: navy;">></a></span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="markdown"></span>
</pre>
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="markdown"><span class="gh" style="color: #999;"># Debugging and troubleshooting</span></span>
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<pre style="margin: 0;"> <span id="LC249" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC250" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Segfaults on certain Intel Xeons</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="305" 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="318" 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">@@ -305,6 +318,8 @@ work on Sambamba, please cite the following publication:</td>
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<td class="diff-line-num old_line" data-linenumber="305" 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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<pre style="margin: 0;"> <span id="LC318" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="306" 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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<pre style="margin: 0;"> <span id="LC319" class="line" lang="markdown">A. Tarasov, A. J. Vilella, E. Cuppen, I. J. Nijman, and P. Prins. <span class="p">[</span><span class="nv" style="color: teal;">Sambamba: fast processing of NGS alignment formats</span><span class="p">](</span><span class="sx" style="color: #d14;">https://doi.org/10.1093/bioinformatics/btv098</span><span class="p">)</span>. Bioinformatics, 2015.</span>
</pre>
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<pre style="margin: 0;"> <span id="LC320" class="line" lang="markdown"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Bibtex reference</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="markdown"></span>
</pre>
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<pre style="margin: 0;"> <span id="LC323" class="line" lang="markdown"><span class="p">```</span><span class="nl">bibtex</span></span>
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<pre style="margin: 0;"> <span id="LC324" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="310" 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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<pre style="margin: 0;"> <span id="LC325" class="line" lang="markdown"><span class="sb" style="color: #d14;">@article{doi:10.1093/bioinformatics/btv098,</span></span>
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<br>
</li>
<li id="6f8a88f369eae9b2f3ece90d1ba6366a16f25f9c">
<a href="https://salsa.debian.org/med-team/sambamba/commit/22dc4a7940dc5de9eada1184d972cdcab89ba973#6f8a88f369eae9b2f3ece90d1ba6366a16f25f9c"><strong>RELEASE-NOTES.md</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## ChangeLog v0.6.8<span class="idiff left right">-pre1 (20180207</span>)</span></span>
</pre>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## ChangeLog v0.6.8<span class="idiff left right"> (20181004</span>)</span></span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="3" 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">
3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="markdown">Minor release with a much faster binary. 10-20% faster than v0.6.6,</span>
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<td class="diff-line-num old old_line" data-linenumber="4" 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">
4
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<td class="diff-line-num new_line old" data-linenumber="3" 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="LC4" class="line" lang="markdown">due to ldc and LLVM improvements. Fixes speed regression of v0.6.7 for</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="markdown">large files. See also <span class="p">[</span><span class="nv" style="color: teal;">performance</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/biod/sambamba/blob/master/test/benchmark/stats.org</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown">Pre-release with a much faster statically compiled binary. 10-20%</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown">faster than v0.6.6, due to ldc and LLVM improvements. Fixes speed</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown">regression of v0.6.7 for large files due to singleobj compilation. See</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown">also #345 and</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">performance</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/biod/sambamba/blob/master/test/benchmark/stats.org</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown">64-bit compilation should be fine on ldc 1.10+. i386 target is still a problem.</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown"><span class="p">+</span> Fix mark duplicates in files with many contigs, see #361 (thanks Devon Ryan @dpryan79)</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown"><span class="p">+</span> Fix missing PM tag in #356 (thanks Kurt Hetrick @Kurt-Hetrick)</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="markdown"><span class="p">+</span> Fix Bcftools version checking #352 (thanks Nathan S. Watson-Haigh @nathanhaigh)</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="markdown"><span class="p">+</span> Fixate version info in BAM output headers for reproducibility. See #357</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="markdown"><span class="p">+</span> Fixed Makefile for general use, see #332</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="markdown"><span class="p">+</span> Started benchmarking, see #283 and https://github.com/biod/sambamba/blob/master/test/benchmark/stats.org</span>
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<td class="diff-line-num 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">
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="markdown"><span class="p">+</span> Readded <span class="p">[</span><span class="nv" style="color: teal;">Travis-ci support</span><span class="p">](</span><span class="sx" style="color: #d14;">https://travis-ci.org/biod/sambamba</span><span class="p">)</span> for Linux (MacOS is disabled #338)</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="markdown"><span class="p">+</span> Fixed MacOS build in Travis with ae269cfbdf2e78750ce7f8dc70ad32f80a6682df</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="markdown"><span class="p">+</span> Updated BioD to latest https://github.com/biod/BioD/commit/5e56b2bb45324af2194b3339d298fd827c8003ae</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="markdown"><span class="p">+</span> Bug fixes:</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="markdown"><span class="p"> *</span> #328 Debug version: SAM output of CRAM file is populated with debug on pipe</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="markdown"><span class="p"> *</span> #331 Segmentation fault attempting to view header in json format</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="markdown"><span class="p"> *</span> #335 Intel Xeon bug may segfault Sambamba - this was tracked down to an Intel Xeon bug</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="markdown"><span class="p"> *</span> #345 sambamba index 0.6.7 takes 4x longer than 0.6.6 on the same files</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="markdown"><span class="p">+</span> Documentation updates</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="markdown"><span class="p">+</span> Updated lz4 to latest (still source in tree because Debian dropped frame support in liblz4-dev)</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="markdown"><span class="p">+</span> Added support for GNU Guix and build containers</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="markdown"><span class="p">+</span> Added shunit2 to the source tree for testing</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="markdown"><span class="p">+</span> Update python build dependencies to use python3.x</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="markdown"><span class="p">+</span> Fixed a number of D compiler messages on deprecated features (ldc 1.11)</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="markdown">To install the image, download and</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="markdown"><span class="p">```</span><span class="nl">sh</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">md5sum </span>sambamba-0.6.8.gz</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="markdown">25efb5604ae5fe7c750e8020326787c5 sambamba-0.8.6.gz</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">gzip</span> <span class="nt" style="color: navy;">-d</span> sambamba-0.6.8.gz</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">chmod </span>a+x sambamba-0.6.8</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="markdown">./sambamba-0.8.6</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="markdown"></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="markdown">sambamba 0.6.8 by Artem Tarasov and Pjotr Prins <span class="o" style="font-weight: 600;">(</span>C<span class="o" style="font-weight: 600;">)</span> 2012-2018</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="markdown"> LDC 1.10.0 / DMD v2.080.1 / LLVM6.0.1 / bootstrap LDC - the LLVM D compiler <span class="o" style="font-weight: 600;">(</span>0.17.4<span class="o" style="font-weight: 600;">)</span></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="markdown"><span class="p">```</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="markdown"></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="markdown">The binary images were reproducibly built on x86_64 with</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="markdown"></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="markdown"><span class="p">```</span><span class="nl">sh</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="markdown">~/.config/guix/current/bin/guix pull <span class="nt" style="color: navy;">-l</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="markdown">Generation 3 Sep 25 2018 09:39:08</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="markdown"> guix 932839f</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="markdown"> repository URL: https://git.savannah.gnu.org/git/guix.git</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="markdown"> branch: origin/master</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="markdown"> commit: 932839ff124ff3b0dd3070914fb1c5beec69bf32</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="markdown">guix environment <span class="nt" style="color: navy;">-C</span> guix <span class="nt" style="color: navy;">--ad-hoc</span> gcc gdb bash ld-wrapper ldc which python git</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="markdown">make clean <span class="o" style="font-weight: 600;">&&</span> make <span class="nt" style="color: navy;">-j</span> 16 <span class="o" style="font-weight: 600;">&&</span> make check</span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="markdown"><span class="k" style="font-weight: 600;">for </span>x <span class="k" style="font-weight: 600;">in</span> <span class="sb" style="color: #d14;">`</span>ldd bin/sambamba|cut <span class="nt" style="color: navy;">-d</span> <span class="s1" style="color: #d14;">' '</span> <span class="nt" style="color: navy;">-f</span> 3<span class="sb" style="color: #d14;">`</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">do </span><span class="nb" style="color: #0086b3;">realpath</span> <span class="nv" style="color: teal;">$x</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">done</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="markdown">/gnu/store/l4lr0f5cjd0nbsaaf8b5dmcw1a1yypr3-glibc-2.27/lib/libpthread-2.27.so</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="markdown">/gnu/store/l4lr0f5cjd0nbsaaf8b5dmcw1a1yypr3-glibc-2.27/lib/libm-2.27.so</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="markdown">/gnu/store/l4lr0f5cjd0nbsaaf8b5dmcw1a1yypr3-glibc-2.27/lib/librt-2.27.so</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="markdown">/gnu/store/l4lr0f5cjd0nbsaaf8b5dmcw1a1yypr3-glibc-2.27/lib/libdl-2.27.so</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="markdown">/gnu/store/bmaxmigwnlbdpls20px2ipq1fll36ncd-gcc-8.2.0-lib/lib/libgcc_s.so.1</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="markdown">/gnu/store/l4lr0f5cjd0nbsaaf8b5dmcw1a1yypr3-glibc-2.27/lib/libc-2.27.so</span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="markdown"><span class="c" style="color: #998; font-style: italic;"># build static image</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="markdown">make clean <span class="o" style="font-weight: 600;">&&</span> make release <span class="nt" style="color: navy;">-j</span> 16 <span class="o" style="font-weight: 600;">&&</span> make check</span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="markdown">Git submodule versions were</span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="markdown"><span class="sb" style="color: #d14;">```</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="markdown"><span class="sb" style="color: #d14;"> git submodule status</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="markdown"><span class="sb" style="color: #d14;"> 2f0634b187e0f454809432093238cf31e9fbfee6 BioD (v0.2.0-5-g2f0634b)</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="markdown"><span class="sb" style="color: #d14;"> 2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5 htslib (0.2.0-rc10-271-g2f3c3ea)</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="markdown"><span class="sb" style="color: #d14;"> b3692db46d2b23a7c0af2d5e69988c94f126e10a lz4 (v1.8.2)</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="markdown"><span class="sb" style="color: #d14;"> 9be93876982b5f14fcca60832563b3cd767dd84d undeaD (v1.0.1-49-g9be9387)</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="markdown"><span class="sb" style="color: #d14;"> ```</span></span></pre>
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<li id="ee1c3381ed1e67657ca0073d77279ffa7aed97fa">
<a href="https://salsa.debian.org/med-team/sambamba/commit/22dc4a7940dc5de9eada1184d972cdcab89ba973#ee1c3381ed1e67657ca0073d77279ffa7aed97fa"><strong>contrib/shunit2-2.0.3/CHANGES-2.0.txt</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">CHANGES WITH 2.0.4</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Unset additional variables that were missed.</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">Fixed off-by-one in exit value for scripts caught by the trap handler.</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">The library did not fail gracefully when the 'od' command was not installed.</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></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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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">CHANGES WITH 2.0.3</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Back ported the Makefile from 2.1.1pre that included changes to the</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">docs-docbook-prep target.</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">Changed the test in assertFalse() so that any non-zero value registers as</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">false. (Credits to Bryan Larsen)</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">Updated the testPartyLikeItIs1999() function in the Quick Start documentation.</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">The 'expected' and 'actual' values were swapped. (Credits to Richard Jensen)</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">It was pointed out that the simple 'failed' message for a failed assert was not</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">only insufficient, it was nonstandard (when compared to JUnit) and didn't</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">provide the user with an expected vs actual result. The code was revised</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">somewhat to bring closer into alignment with JUnit (v4.3.1 specifically) so</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">that it feels more "normal". (Credits to Richard Jensen)</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">As part of the JUnit realignment, it was noticed that fail*() functions in</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">JUnit don't actually do any comparisons themselves. They only generate a</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">failure message. Updated the code to match.</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">Added self-testing unit tests. Kinda horkey, but they did find bugs during the</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">JUnit realignment.</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">Fixed the code for returning from asserts as the return was being called before</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">the unsetting of variables occurred. (Credits to Mathias Goldau)</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">The assert(True|False)() functions now accept an integer value for a</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">conditional test. A value of '0' is considered 'true', while any non-zero value</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">is considered 'false'.</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">All public functions now fill use default values to work properly with the '-x'</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">shell debugging flag.</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">Fixed the method of percent calculation for the report to get achieve better</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">accuracy.</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="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">CHANGES WITH 2.0.2</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">Fixed problem with fail(). The failure message was not properly printed.</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">Reworked the Makefile so that the DocBook XML and XSLT files are properly</span>
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<td class="diff-line-num new new_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">downloaded before parsing can continue.</span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext"></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext"></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">CHANGES WITH 2.0.1</span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">Fixed some really stupid mistakes with the fail* functions. They were doing the</span>
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<td class="diff-line-num new new_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">exact opposite of what they were supposed to be doing.</span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext"></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">CHANGES WITH 2.0.0</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext"></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">Made the first stand-alone release!</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext"></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext"></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">$Revision$</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">vim:spell</span></pre>
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<li id="c1b849a10472129e8da39d120c4193d65bb4ddb1">
<a href="https://salsa.debian.org/med-team/sambamba/commit/22dc4a7940dc5de9eada1184d972cdcab89ba973#c1b849a10472129e8da39d120c4193d65bb4ddb1"><strong>contrib/shunit2-2.0.3/LGPL-2.1</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"> GNU LESSER GENERAL PUBLIC LICENSE</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"> Version 2.1, February 1999</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> Copyright (C) 1991, 1999 Free Software Foundation, Inc.</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> Everyone is permitted to copy and distribute verbatim copies</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> of this license document, but changing it is not allowed.</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">[This is the first released version of the Lesser GPL. It also counts</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> as the successor of the GNU Library Public License, version 2, hence</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> the version number 2.1.]</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> Preamble</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> The licenses for most software are designed to take away your</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">freedom to share and change it. By contrast, the GNU General Public</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">Licenses are intended to guarantee your freedom to share and change</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">free software--to make sure the software is free for all its users.</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> This license, the Lesser General Public License, applies to some</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">specially designated software packages--typically libraries--of the</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">Free Software Foundation and other authors who decide to use it. You</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">can use it too, but we suggest you first think carefully about whether</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">this license or the ordinary General Public License is the better</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">strategy to use in any particular case, based on the explanations below.</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> When we speak of free software, we are referring to freedom of use,</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">not price. Our General Public Licenses are designed to make sure that</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">you have the freedom to distribute copies of free software (and charge</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">for this service if you wish); that you receive source code or can get</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">it if you want it; that you can change the software and use pieces of</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">it in new free programs; and that you are informed that you can do</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">these things.</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> To protect your rights, we need to make restrictions that forbid</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">distributors to deny you these rights or to ask you to surrender these</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">rights. These restrictions translate to certain responsibilities for</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">you if you distribute copies of the library or if you modify it.</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> For example, if you distribute copies of the library, whether gratis</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">or for a fee, you must give the recipients all the rights that we gave</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">you. You must make sure that they, too, receive or can get the source</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">code. If you link other code with the library, you must provide</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">complete object files to the recipients, so that they can relink them</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">with the library after making changes to the library and recompiling</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">it. And you must show them these terms so they know their rights.</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"> We protect your rights with a two-step method: (1) we copyright the</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">library, and (2) we offer you this license, which gives you legal</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">permission to copy, distribute and/or modify the library.</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"> To protect each distributor, we want to make it very clear that</span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">there is no warranty for the free library. Also, if the library is</span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">modified by someone else and passed on, the recipients should know</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">that what they have is not the original version, so that the original</span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">author's reputation will not be affected by problems that might be</span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">introduced by others.</span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext"></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext"> Finally, software patents pose a constant threat to the existence of</span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">any free program. We wish to make sure that a company cannot</span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">effectively restrict the users of a free program by obtaining a</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">restrictive license from a patent holder. Therefore, we insist that</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">any patent license obtained for a version of the library must be</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">consistent with the full freedom of use specified in this license.</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext"></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext"> Most GNU software, including some libraries, is covered by the</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">ordinary GNU General Public License. This license, the GNU Lesser</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">General Public License, applies to certain designated libraries, and</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext">is quite different from the ordinary General Public License. We use</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">this license for certain libraries in order to permit linking those</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext">libraries into non-free programs.</span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext"></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext"> When a program is linked with a library, whether statically or using</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext">a shared library, the combination of the two is legally speaking a</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext">combined work, a derivative of the original library. The ordinary</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext">General Public License therefore permits such linking only if the</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext">entire combination fits its criteria of freedom. The Lesser General</span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext">Public License permits more lax criteria for linking other code with</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext">the library.</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext"></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext"> We call this license the "Lesser" General Public License because it</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext">does Less to protect the user's freedom than the ordinary General</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext">Public License. It also provides other free software developers Less</span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext">of an advantage over competing non-free programs. These disadvantages</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext">are the reason we use the ordinary General Public License for many</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext">libraries. However, the Lesser license provides advantages in certain</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext">special circumstances.</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext"></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext"> For example, on rare occasions, there may be a special need to</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext">encourage the widest possible use of a certain library, so that it becomes</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext">a de-facto standard. To achieve this, non-free programs must be</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext">allowed to use the library. A more frequent case is that a free</span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext">library does the same job as widely used non-free libraries. In this</span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext">case, there is little to gain by limiting the free library to free</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext">software only, so we use the Lesser General Public License.</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext"></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext"> In other cases, permission to use a particular library in non-free</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext">programs enables a greater number of people to use a large body of</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext">free software. For example, permission to use the GNU C Library in</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext">non-free programs enables many more people to use the whole GNU</span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext">operating system, as well as its variant, the GNU/Linux operating</span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext">system.</span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext"></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext"> Although the Lesser General Public License is Less protective of the</span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext">users' freedom, it does ensure that the user of a program that is</span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext">linked with the Library has the freedom and the wherewithal to run</span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext">that program using a modified version of the Library.</span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext"></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext"> The precise terms and conditions for copying, distribution and</span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext">modification follow. Pay close attention to the difference between a</span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext">"work based on the library" and a "work that uses the library". The</span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext">former contains code derived from the library, whereas the latter must</span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext">be combined with the library in order to run.</span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext"></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext"> GNU LESSER GENERAL PUBLIC LICENSE</span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext"> TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION</span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext"></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext"> 0. This License Agreement applies to any software library or other</span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext">program which contains a notice placed by the copyright holder or</span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext">other authorized party saying it may be distributed under the terms of</span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext">this Lesser General Public License (also called "this License").</span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="plaintext">Each licensee is addressed as "you".</span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext"></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext"> A "library" means a collection of software functions and/or data</span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="plaintext">prepared so as to be conveniently linked with application programs</span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="plaintext">(which use some of those functions and data) to form executables.</span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="plaintext"></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="plaintext"> The "Library", below, refers to any such software library or work</span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="plaintext">which has been distributed under these terms. A "work based on the</span>
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<td class="diff-line-num new new_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="plaintext">Library" means either the Library or any derivative work under</span>
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<td class="diff-line-num new new_line" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="plaintext">copyright law: that is to say, a work containing the Library or a</span>
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<td class="diff-line-num new new_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="plaintext">portion of it, either verbatim or with modifications and/or translated</span>
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<td class="diff-line-num new new_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="plaintext">straightforwardly into another language. (Hereinafter, translation is</span>
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<td class="diff-line-num new new_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext">included without limitation in the term "modification".)</span>
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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"></span>
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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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<pre style="margin: 0;">+<span id="LC136" class="line" lang="plaintext"> "Source code" for a work means the preferred form of the work for</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="plaintext">making modifications to it. For a library, complete source code means</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="plaintext">all the source code for all modules it contains, plus any associated</span>
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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="plaintext">interface definition files, plus the scripts used to control compilation</span>
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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="plaintext">and installation of the library.</span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="plaintext"></span>
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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
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="plaintext"> Activities other than copying, distribution and modification are not</span>
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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
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="plaintext">covered by this License; they are outside its scope. The act of</span>
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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">running a program using the Library is not restricted, and output from</span>
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<td class="diff-line-num new new_line" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="plaintext">such a program is covered only if its contents constitute a work based</span>
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<td class="diff-line-num new new_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="plaintext">on the Library (independent of the use of the Library in a tool for</span>
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<td class="diff-line-num new new_line" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="plaintext">writing it). Whether that is true depends on what the Library does</span>
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<td class="diff-line-num new new_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="plaintext">and what the program that uses the Library does.</span>
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<td class="diff-line-num new new_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="plaintext"> </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"> 1. You may copy and distribute verbatim copies of the Library's</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">complete source code as you receive it, in any medium, provided that</span>
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<td class="diff-line-num new new_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="plaintext">you conspicuously and appropriately publish on each copy an</span>
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<td class="diff-line-num new new_line" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="plaintext">appropriate copyright notice and disclaimer of warranty; keep intact</span>
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<td class="diff-line-num new new_line" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="plaintext">all the notices that refer to this License and to the absence of any</span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="plaintext">warranty; and distribute a copy of this License along with the</span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="plaintext">Library.</span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="plaintext"></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="plaintext"> You may charge a fee for the physical act of transferring a copy,</span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="plaintext">and you may at your option offer warranty protection in exchange for a</span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="plaintext">fee.</span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="plaintext"> 2. You may modify your copy or copies of the Library or any portion</span>
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<td class="diff-line-num new new_line" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="plaintext">of it, thus forming a work based on the Library, and copy and</span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="plaintext">distribute such modifications or work under the terms of Section 1</span>
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<td class="diff-line-num new new_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="plaintext">above, provided that you also meet all of these conditions:</span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="plaintext"></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="plaintext"> a) The modified work must itself be a software library.</span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="plaintext"></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="plaintext"> b) You must cause the files modified to carry prominent notices</span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="plaintext"> stating that you changed the files and the date of any change.</span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="plaintext"> c) You must cause the whole of the work to be licensed at no</span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="plaintext"> charge to all third parties under the terms of this License.</span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="plaintext"> d) If a facility in the modified Library refers to a function or a</span>
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<td class="diff-line-num new new_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="plaintext"> table of data to be supplied by an application program that uses</span>
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<td class="diff-line-num new new_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="plaintext"> the facility, other than as an argument passed when the facility</span>
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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"> is invoked, then you must make a good faith effort to ensure that,</span>
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<td class="diff-line-num new new_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="plaintext"> in the event an application does not supply such function or</span>
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<td class="diff-line-num new new_line" data-linenumber="180" style="width: 35px; color: rgba(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="LC180" class="line" lang="plaintext"> table, the facility still operates, and performs whatever part of</span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="plaintext"> its purpose remains meaningful.</span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="plaintext"> (For example, a function in a library to compute square roots has</span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="plaintext"> a purpose that is entirely well-defined independent of the</span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="plaintext"> application. Therefore, Subsection 2d requires that any</span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="plaintext"> application-supplied function or table used by this function must</span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="plaintext"> be optional: if the application does not supply it, the square</span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="plaintext"> root function must still compute square roots.)</span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="plaintext"></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="plaintext">These requirements apply to the modified work as a whole. If</span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="plaintext">identifiable sections of that work are not derived from the Library,</span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="plaintext">and can be reasonably considered independent and separate works in</span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="plaintext">themselves, then this License, and its terms, do not apply to those</span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="plaintext">sections when you distribute them as separate works. But when you</span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="plaintext">distribute the same sections as part of a whole which is a work based</span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="plaintext">on the Library, the distribution of the whole must be on the terms of</span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="plaintext">this License, whose permissions for other licensees extend to the</span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="plaintext">entire whole, and thus to each and every part regardless of who wrote</span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="plaintext">it.</span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="plaintext"></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="plaintext">Thus, it is not the intent of this section to claim rights or contest</span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="plaintext">your rights to work written entirely by you; rather, the intent is to</span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="plaintext">exercise the right to control the distribution of derivative or</span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="plaintext">collective works based on the Library.</span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="plaintext">In addition, mere aggregation of another work not based on the Library</span>
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<td class="diff-line-num new new_line" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="plaintext">with the Library (or with a work based on the Library) on a volume of</span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="plaintext">a storage or distribution medium does not bring the other work under</span>
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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">the scope of this License.</span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="plaintext"></span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="plaintext"> 3. You may opt to apply the terms of the ordinary GNU General Public</span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="plaintext">License instead of this License to a given copy of the Library. To do</span>
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<td class="diff-line-num new new_line" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="plaintext">this, you must alter all the notices that refer to this License, so</span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="plaintext">that they refer to the ordinary GNU General Public License, version 2,</span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="plaintext">instead of to this License. (If a newer version than version 2 of the</span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="plaintext">ordinary GNU General Public License has appeared, then you can specify</span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="plaintext">that version instead if you wish.) Do not make any other change in</span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="plaintext">these notices.</span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="plaintext"></span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="plaintext"> Once this change is made in a given copy, it is irreversible for</span>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="plaintext">that copy, so the ordinary GNU General Public License applies to all</span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="plaintext">subsequent copies and derivative works made from that copy.</span>
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223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="plaintext"></span>
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224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="plaintext"> This option is useful when you wish to copy part of the code of</span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="plaintext">the Library into a program that is not a library.</span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="plaintext"> 4. You may copy and distribute the Library (or a portion or</span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="plaintext">derivative of it, under Section 2) in object code or executable form</span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="plaintext">under the terms of Sections 1 and 2 above provided that you accompany</span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="plaintext">it with the complete corresponding machine-readable source code, which</span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="plaintext">must be distributed under the terms of Sections 1 and 2 above on a</span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="plaintext">medium customarily used for software interchange.</span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="plaintext"> If distribution of object code is made by offering access to copy</span>
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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="plaintext">from a designated place, then offering equivalent access to copy the</span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="plaintext">source code from the same place satisfies the requirement to</span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="plaintext">distribute the source code, even though third parties are not</span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="plaintext">compelled to copy the source along with the object code.</span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="plaintext"> 5. A program that contains no derivative of any portion of the</span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="plaintext">Library, but is designed to work with the Library by being compiled or</span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="plaintext">linked with it, is called a "work that uses the Library". Such a</span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="plaintext">work, in isolation, is not a derivative work of the Library, and</span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="plaintext">therefore falls outside the scope of this License.</span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="plaintext"> However, linking a "work that uses the Library" with the Library</span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="plaintext">creates an executable that is a derivative of the Library (because it</span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="plaintext">contains portions of the Library), rather than a "work that uses the</span>
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="plaintext">library". The executable is therefore covered by this License.</span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="plaintext">Section 6 states terms for distribution of such executables.</span>
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251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="plaintext"> When a "work that uses the Library" uses material from a header file</span>
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<td class="diff-line-num new new_line" data-linenumber="253" style="width: 35px; color: rgba(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="LC253" class="line" lang="plaintext">that is part of the Library, the object code for the work may be a</span>
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<td class="diff-line-num new new_line" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="plaintext">derivative work of the Library even though the source code is not.</span>
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="plaintext">Whether this is true is especially significant if the work can be</span>
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<td class="diff-line-num new new_line" data-linenumber="256" style="width: 35px; color: rgba(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="LC256" class="line" lang="plaintext">linked without the Library, or if the work is itself a library. The</span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="plaintext">threshold for this to be true is not precisely defined by law.</span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="plaintext"></span>
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259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="plaintext"> If such an object file uses only numerical parameters, data</span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="plaintext">structure layouts and accessors, and small macros and small inline</span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="plaintext">functions (ten lines or less in length), then the use of the object</span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="plaintext">file is unrestricted, regardless of whether it is legally a derivative</span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="plaintext">work. (Executables containing this object code plus portions of the</span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="plaintext">Library will still fall under Section 6.)</span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="plaintext"></span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="plaintext"> Otherwise, if the work is a derivative of the Library, you may</span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="plaintext">distribute the object code for the work under the terms of Section 6.</span>
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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="plaintext">Any executables containing that work also fall under Section 6,</span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="plaintext">whether or not they are linked directly with the Library itself.</span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="plaintext"></span>
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="plaintext"> 6. As an exception to the Sections above, you may also combine or</span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="plaintext">link a "work that uses the Library" with the Library to produce a</span>
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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="plaintext">work containing portions of the Library, and distribute that work</span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="plaintext">under terms of your choice, provided that the terms permit</span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="plaintext">modification of the work for the customer's own use and reverse</span>
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="plaintext">engineering for debugging such modifications.</span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="plaintext"> You must give prominent notice with each copy of the work that the</span>
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<td class="diff-line-num new new_line" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="plaintext">Library is used in it and that the Library and its use are covered by</span>
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<td class="diff-line-num new new_line" data-linenumber="280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="plaintext">this License. You must supply a copy of this License. If the work</span>
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<td class="diff-line-num new new_line" data-linenumber="281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="plaintext">during execution displays copyright notices, you must include the</span>
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<td class="diff-line-num new new_line" data-linenumber="282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="plaintext">copyright notice for the Library among them, as well as a reference</span>
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<td class="diff-line-num new new_line" data-linenumber="283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="plaintext">directing the user to the copy of this License. Also, you must do one</span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="plaintext">of these things:</span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="plaintext"></span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="plaintext"> a) Accompany the work with the complete corresponding</span>
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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="plaintext"> machine-readable source code for the Library including whatever</span>
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288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="plaintext"> changes were used in the work (which must be distributed under</span>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="plaintext"> Sections 1 and 2 above); and, if the work is an executable linked</span>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="plaintext"> with the Library, with the complete machine-readable "work that</span>
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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="plaintext"> uses the Library", as object code and/or source code, so that the</span>
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292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="plaintext"> user can modify the Library and then relink to produce a modified</span>
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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="plaintext"> executable containing the modified Library. (It is understood</span>
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294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="plaintext"> that the user who changes the contents of definitions files in the</span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="plaintext"> Library will not necessarily be able to recompile the application</span>
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="plaintext"> to use the modified definitions.)</span>
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297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="plaintext"></span>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="plaintext"> b) Use a suitable shared library mechanism for linking with the</span>
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299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="plaintext"> Library. A suitable mechanism is one that (1) uses at run time a</span>
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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="plaintext"> copy of the library already present on the user's computer system,</span>
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301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="plaintext"> rather than copying library functions into the executable, and (2)</span>
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302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="plaintext"> will operate properly with a modified version of the library, if</span>
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="plaintext"> the user installs one, as long as the modified version is</span>
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="plaintext"> interface-compatible with the version that the work was made with.</span>
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="plaintext"> c) Accompany the work with a written offer, valid for at</span>
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="plaintext"> least three years, to give the same user the materials</span>
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<td class="diff-line-num new new_line" data-linenumber="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="plaintext"> specified in Subsection 6a, above, for a charge no more</span>
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<td class="diff-line-num new new_line" data-linenumber="309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="plaintext"> than the cost of performing this distribution.</span>
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310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="311" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="plaintext"> d) If distribution of the work is made by offering access to copy</span>
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<td class="diff-line-num new new_line" data-linenumber="312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="plaintext"> from a designated place, offer equivalent access to copy the above</span>
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313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="plaintext"> specified materials from the same place.</span>
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314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="plaintext"></span>
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315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="plaintext"> e) Verify that the user has already received a copy of these</span>
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316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="plaintext"> materials or that you have already sent this user a copy.</span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="plaintext"></span>
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318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="plaintext"> For an executable, the required form of the "work that uses the</span>
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319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="plaintext">Library" must include any data and utility programs needed for</span>
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="plaintext">reproducing the executable from it. However, as a special exception,</span>
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321
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="plaintext">the materials to be distributed need not include anything that is</span>
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322
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="plaintext">normally distributed (in either source or binary form) with the major</span>
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323
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="plaintext">components (compiler, kernel, and so on) of the operating system on</span>
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="plaintext">which the executable runs, unless that component itself accompanies</span>
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325
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="plaintext">the executable.</span>
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="plaintext"></span>
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327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="plaintext"> It may happen that this requirement contradicts the license</span>
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328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="plaintext">restrictions of other proprietary libraries that do not normally</span>
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329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="plaintext">accompany the operating system. Such a contradiction means you cannot</span>
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330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="plaintext">use both them and the Library together in an executable that you</span>
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331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="plaintext">distribute.</span>
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="plaintext"> 7. You may place library facilities that are a work based on the</span>
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334
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="plaintext">Library side-by-side in a single library together with other library</span>
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335
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="plaintext">facilities not covered by this License, and distribute such a combined</span>
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336
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="plaintext">library, provided that the separate distribution of the work based on</span>
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337
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="plaintext">the Library and of the other library facilities is otherwise</span>
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338
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="plaintext">permitted, and provided that you do these two things:</span>
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="plaintext"> a) Accompany the combined library with a copy of the same work</span>
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341
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="plaintext"> based on the Library, uncombined with any other library</span>
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="plaintext"> facilities. This must be distributed under the terms of the</span>
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343
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="plaintext"> Sections above.</span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="plaintext"> b) Give prominent notice with the combined library of the fact</span>
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="plaintext"> that part of it is a work based on the Library, and explaining</span>
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="plaintext"> where to find the accompanying uncombined form of the same work.</span>
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348
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="plaintext"> 8. You may not copy, modify, sublicense, link with, or distribute</span>
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="plaintext">the Library except as expressly provided under this License. Any</span>
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="plaintext">attempt otherwise to copy, modify, sublicense, link with, or</span>
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="plaintext">distribute the Library is void, and will automatically terminate your</span>
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="plaintext">rights under this License. However, parties who have received copies,</span>
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="plaintext">or rights, from you under this License will not have their licenses</span>
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="plaintext">terminated so long as such parties remain in full compliance.</span>
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="plaintext"> 9. You are not required to accept this License, since you have not</span>
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="plaintext">signed it. However, nothing else grants you permission to modify or</span>
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359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="plaintext">distribute the Library or its derivative works. These actions are</span>
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360
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="plaintext">prohibited by law if you do not accept this License. Therefore, by</span>
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361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="plaintext">modifying or distributing the Library (or any work based on the</span>
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<td class="diff-line-num new new_line" data-linenumber="362" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="plaintext">Library), you indicate your acceptance of this License to do so, and</span>
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363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="plaintext">all its terms and conditions for copying, distributing or modifying</span>
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<td class="diff-line-num new new_line" data-linenumber="364" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
364
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="plaintext">the Library or works based on it.</span>
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365
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="plaintext"></span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="plaintext"> 10. Each time you redistribute the Library (or any work based on the</span>
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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="plaintext">Library), the recipient automatically receives a license from the</span>
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368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="plaintext">original licensor to copy, distribute, link with or modify the Library</span>
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369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="plaintext">subject to these terms and conditions. You may not impose any further</span>
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370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="plaintext">restrictions on the recipients' exercise of the rights granted herein.</span>
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<td class="diff-line-num new new_line" data-linenumber="371" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="plaintext">You are not responsible for enforcing compliance by third parties with</span>
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372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="plaintext">this License.</span>
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373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="plaintext"></span>
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374
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="plaintext"> 11. If, as a consequence of a court judgment or allegation of patent</span>
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375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="plaintext">infringement or for any other reason (not limited to patent issues),</span>
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<td class="diff-line-num new new_line" data-linenumber="376" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="plaintext">conditions are imposed on you (whether by court order, agreement or</span>
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<td class="diff-line-num new new_line" data-linenumber="377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="plaintext">otherwise) that contradict the conditions of this License, they do not</span>
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<td class="diff-line-num new new_line" data-linenumber="378" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
378
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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="LC378" class="line" lang="plaintext">excuse you from the conditions of this License. If you cannot</span>
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<td class="diff-line-num new new_line" data-linenumber="379" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="plaintext">distribute so as to satisfy simultaneously your obligations under this</span>
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<td class="diff-line-num new new_line" data-linenumber="380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="plaintext">License and any other pertinent obligations, then as a consequence you</span>
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<td class="diff-line-num new new_line" data-linenumber="381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="plaintext">may not distribute the Library at all. For example, if a patent</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="382" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="plaintext">license would not permit royalty-free redistribution of the Library by</span>
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<td class="diff-line-num new new_line" data-linenumber="383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="plaintext">all those who receive copies directly or indirectly through you, then</span>
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<td class="diff-line-num new new_line" data-linenumber="384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="plaintext">the only way you could satisfy both it and this License would be to</span>
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<td class="diff-line-num new new_line" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="plaintext">refrain entirely from distribution of the Library.</span>
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<td class="diff-line-num new new_line" data-linenumber="386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="387" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="plaintext">If any portion of this section is held invalid or unenforceable under any</span>
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<td class="diff-line-num new new_line" data-linenumber="388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="plaintext">particular circumstance, the balance of the section is intended to apply,</span>
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<td class="diff-line-num new new_line" data-linenumber="389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="plaintext">and the section as a whole is intended to apply in other circumstances.</span>
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<td class="diff-line-num new new_line" data-linenumber="390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="plaintext">It is not the purpose of this section to induce you to infringe any</span>
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<td class="diff-line-num new new_line" data-linenumber="392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="plaintext">patents or other property right claims or to contest validity of any</span>
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="plaintext">such claims; this section has the sole purpose of protecting the</span>
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<td class="diff-line-num new new_line" data-linenumber="394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="plaintext">integrity of the free software distribution system which is</span>
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<td class="diff-line-num new new_line" data-linenumber="395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="plaintext">implemented by public license practices. Many people have made</span>
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<td class="diff-line-num new new_line" data-linenumber="396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="plaintext">generous contributions to the wide range of software distributed</span>
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397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="plaintext">through that system in reliance on consistent application of that</span>
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<td class="diff-line-num new new_line" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="plaintext">system; it is up to the author/donor to decide if he or she is willing</span>
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<td class="diff-line-num new new_line" data-linenumber="399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="plaintext">to distribute software through any other system and a licensee cannot</span>
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400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="plaintext">impose that choice.</span>
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401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="plaintext">This section is intended to make thoroughly clear what is believed to</span>
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<td class="diff-line-num new new_line" data-linenumber="403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
403
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="plaintext">be a consequence of the rest of this License.</span>
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404
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
405
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="plaintext"> 12. If the distribution and/or use of the Library is restricted in</span>
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<td class="diff-line-num new new_line" data-linenumber="406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
406
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="plaintext">certain countries either by patents or by copyrighted interfaces, the</span>
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<td class="diff-line-num new new_line" data-linenumber="407" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
407
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="plaintext">original copyright holder who places the Library under this License may add</span>
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<td class="diff-line-num new new_line" data-linenumber="408" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
408
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="plaintext">an explicit geographical distribution limitation excluding those countries,</span>
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409
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="plaintext">so that distribution is permitted only in or among countries not thus</span>
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410
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="plaintext">excluded. In such case, this License incorporates the limitation as if</span>
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411
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="plaintext">written in the body of this License.</span>
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412
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="plaintext"></span>
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413
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="plaintext"> 13. The Free Software Foundation may publish revised and/or new</span>
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<td class="diff-line-num new new_line" data-linenumber="414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
414
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="plaintext">versions of the Lesser General Public License from time to time.</span>
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<td class="diff-line-num new new_line" data-linenumber="415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
415
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="plaintext">Such new versions will be similar in spirit to the present version,</span>
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416
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="plaintext">but may differ in detail to address new problems or concerns.</span>
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417
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="plaintext"></span>
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418
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="plaintext">Each version is given a distinguishing version number. If the Library</span>
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419
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="plaintext">specifies a version number of this License which applies to it and</span>
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420
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="plaintext">"any later version", you have the option of following the terms and</span>
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421
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="plaintext">conditions either of that version or of any later version published by</span>
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422
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="plaintext">the Free Software Foundation. If the Library does not specify a</span>
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423
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="plaintext">license version number, you may choose any version ever published by</span>
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424
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="plaintext">the Free Software Foundation.</span>
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425
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="plaintext"></span>
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426
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="plaintext"> 14. If you wish to incorporate parts of the Library into other free</span>
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427
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="plaintext">programs whose distribution conditions are incompatible with these,</span>
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428
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="plaintext">write to the author to ask for permission. For software which is</span>
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429
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="plaintext">copyrighted by the Free Software Foundation, write to the Free</span>
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430
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="plaintext">Software Foundation; we sometimes make exceptions for this. Our</span>
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431
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="plaintext">decision will be guided by the two goals of preserving the free status</span>
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432
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="plaintext">of all derivatives of our free software and of promoting the sharing</span>
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433
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="plaintext">and reuse of software generally.</span>
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="plaintext"></span>
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435
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="plaintext"> NO WARRANTY</span>
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436
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="plaintext"></span>
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437
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="plaintext"> 15. BECAUSE THE LIBRARY IS LICENSED FREE OF CHARGE, THERE IS NO</span>
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438
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="plaintext">WARRANTY FOR THE LIBRARY, TO THE EXTENT PERMITTED BY APPLICABLE LAW.</span>
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439
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="plaintext">EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR</span>
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440
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="plaintext">OTHER PARTIES PROVIDE THE LIBRARY "AS IS" WITHOUT WARRANTY OF ANY</span>
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441
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="plaintext">KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE</span>
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442
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="plaintext">IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR</span>
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443
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="plaintext">PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE</span>
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444
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="plaintext">LIBRARY IS WITH YOU. SHOULD THE LIBRARY PROVE DEFECTIVE, YOU ASSUME</span>
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445
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="plaintext">THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.</span>
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446
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="plaintext"></span>
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447
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="plaintext"> 16. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN</span>
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448
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="plaintext">WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY</span>
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449
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="plaintext">AND/OR REDISTRIBUTE THE LIBRARY AS PERMITTED ABOVE, BE LIABLE TO YOU</span>
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450
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="plaintext">FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR</span>
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451
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="plaintext">CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE</span>
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452
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="plaintext">LIBRARY (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING</span>
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453
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="plaintext">RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A</span>
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454
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="plaintext">FAILURE OF THE LIBRARY TO OPERATE WITH ANY OTHER SOFTWARE), EVEN IF</span>
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455
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="plaintext">SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH</span>
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456
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="plaintext">DAMAGES.</span>
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457
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="plaintext"></span>
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458
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="plaintext"> END OF TERMS AND CONDITIONS</span>
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459
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="plaintext"> How to Apply These Terms to Your New Libraries</span>
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="plaintext"> If you develop a new library, and you want it to be of the greatest</span>
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="plaintext">possible use to the public, we recommend making it free software that</span>
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<pre style="margin: 0;">+<span id="LC464" class="line" lang="plaintext">everyone can redistribute and change. You can do so by permitting</span>
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="plaintext">redistribution under these terms (or, alternatively, under the terms of the</span>
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="plaintext">ordinary General Public License).</span>
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="plaintext"> To apply these terms, attach the following notices to the library. It is</span>
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469
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="plaintext">safest to attach them to the start of each source file to most effectively</span>
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470
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="plaintext">convey the exclusion of warranty; and each file should have at least the</span>
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471
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="plaintext">"copyright" line and a pointer to where the full notice is found.</span>
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472
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="plaintext"></span>
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473
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="plaintext"> <one line to give the library's name and a brief idea of what it does.></span>
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474
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<pre style="margin: 0;">+<span id="LC474" class="line" lang="plaintext"> Copyright (C) <year> <name of author></span>
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475
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="plaintext"></span>
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476
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="plaintext"> This library is free software; you can redistribute it and/or</span>
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477
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="plaintext"> modify it under the terms of the GNU Lesser General Public</span>
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478
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="plaintext"> License as published by the Free Software Foundation; either</span>
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479
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="plaintext"> version 2.1 of the License, or (at your option) any later version.</span>
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480
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="plaintext"></span>
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481
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="plaintext"> This library is distributed in the hope that it will be useful,</span>
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482
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="plaintext"> but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
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483
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<pre style="margin: 0;">+<span id="LC483" class="line" lang="plaintext"> MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU</span>
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484
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="plaintext"> Lesser General Public License for more details.</span>
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486
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="plaintext"> You should have received a copy of the GNU Lesser General Public</span>
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487
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="plaintext"> License along with this library; if not, write to the Free Software</span>
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488
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="plaintext"> Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA</span>
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489
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="plaintext"></span>
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490
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="plaintext">Also add information on how to contact you by electronic and paper mail.</span>
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="plaintext"></span>
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492
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="plaintext">You should also get your employer (if you work as a programmer) or your</span>
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493
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="plaintext">school, if any, to sign a "copyright disclaimer" for the library, if</span>
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="plaintext">necessary. Here is a sample; alter the names:</span>
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495
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="plaintext"></span>
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496
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="plaintext"> Yoyodyne, Inc., hereby disclaims all copyright interest in the</span>
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="plaintext"> library `Frob' (a library for tweaking knobs) written by James Random Hacker.</span>
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="plaintext"> <signature of Ty Coon>, 1 April 1990</span>
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="plaintext"> Ty Coon, President of Vice</span>
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="plaintext">That's all there is to it!</span>
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503
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC504" class="line" lang="plaintext"></span></pre>
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<li id="886d2eab1399ec70ccec5016be01978a97ccca3b">
<a href="https://salsa.debian.org/med-team/sambamba/commit/22dc4a7940dc5de9eada1184d972cdcab89ba973#886d2eab1399ec70ccec5016be01978a97ccca3b"><strong>contrib/shunit2-2.0.3/README.txt</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">#------------------------------------------------------------------------------</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"># SourceForge</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">#</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">This project is stored on SourceForge as http://sf.net/projects/shunit2. The</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">source code can be accessed using the following information.</span>
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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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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">* Subversion</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">$ svn co https://shunit2.svn.sourceforge.net/svnroot/shunit2/trunk/source shunit2</span>
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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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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">Subversion may also be browsed via a web browser at</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">http://svn.sourceforge.net/shunit2</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">#------------------------------------------------------------------------------</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"># Making a release</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">#</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">For these steps, it is assumed we are working with release 2.0.0.</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">Steps:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">* write release notes</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">* update version</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">* finish changelog</span>
</pre>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">* check all the code in</span>
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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">* tag the release</span>
</pre>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">* export the release</span>
</pre>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">* create tarball</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">* md5sum the tarball and sign with gpg</span>
</pre>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">* update website</span>
</pre>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">* post to SourceForge and Freshmeat</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">WRITE RELEASE NOTES</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">This should be pretty self explainatory. Use one of the release notes from a</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">previous release as an example.</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">To get the versions of the various shells, do the following:</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">Cygwin</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"> bash: $ bash --version</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> ksh: actually pdksh</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"> pdksh: look in the downloaded Cygwin directory</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">Linux</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"> bash: $ bash --version</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"> dash: look at installed version</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"> ksh: $ ksh --version</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"> pdksh: $ strings /bin/pdksh |grep 'PD KSH'</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"> zsh: $ zsh --version</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">Solaris 10</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"> sh: not possible</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"> bash: $ bash --version</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"> ksh: $ strings /usr/bin/ksh |grep 'Version'</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">UPDATE VERSION</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">Edit the shunit2 source code, and change the version number in the comment, as</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">well as in the __SHUNIT_VERSION variable. Next, edit the</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">src/docbook/shunit2.xml file, edit the version in the <title> element, and make</span>
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<td class="diff-line-num new new_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">sure there is a revision section for this release.</span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext"></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">FINISH DOCUMENTATION</span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">Make sure that any remaning changes get put into the CHANGES-X.X.txt file.</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext"></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">Finish writing the RELEASE_NOTES-X.X.X.txt. Once it is finished, run it through</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">the 'fmt' command to make it pretty.</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext"></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">$ fmt -w 80 RELEASE_NOTES-2.0.0.txt >RELEASE_NOTES-2.0.0.txt.new</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">$ mv RELEASE_NOTES-2.0.0.txt.new RELEASE_NOTES-2.0.0.txt</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext"></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">We want to have an up-to-date version of the documentation in the release, so</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext">we'd better build it.</span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext"></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">$ pwd</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext">.../shunit2/source/2.0</span>
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<td class="diff-line-num new new_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext">$ make docs</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext">...</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext">$ cp -p build/shunit2.html doc</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext">$ svn ci -m "" doc/shunit2.html</span>
</pre>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext"></span>
</pre>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext">CHECK IN ALL THE CODE</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext"></span>
</pre>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext">This step is pretty self-explainatory</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext">TAG THE RELEASE</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext"></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext">$ pwd</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext">.../shunit2/source</span>
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<td class="diff-line-num new new_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext">$ ls</span>
</pre>
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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="plaintext">2.0 2.1</span>
</pre>
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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="plaintext">$ svn cp -m "Release 2.0.0" \</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext">2.0 https://shunit2.svn.sourceforge.net/svnroot/shunit2/tags/source/2.0.0</span>
</pre>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext">EXPORT THE RELEASE</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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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext"></span>
</pre>
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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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext">$ pwd</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="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext">.../shunit2/builds</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
97
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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="LC97" class="line" lang="plaintext">$ svn export \</span>
</pre>
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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">https://shunit2.svn.sourceforge.net/svnroot/shunit2/tags/source/2.0.0 \</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext">shunit2-2.0.0</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="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext"></span>
</pre>
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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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext">CREATE TARBALL</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">
</td>
<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"></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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext">$ tar cfz ../releases/shunit2-2.0.0.tgz shunit2-2.0.0</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="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"></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="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
105
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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="LC105" class="line" lang="plaintext">MD5SUM THE TARBALL AND SIGN WITH GPG</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">
</td>
<td class="diff-line-num new new_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
106
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<pre style="margin: 0;">+<span id="LC106" 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="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext">$ cd ../releases</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">$ md5sum shunit2-2.0.0.tgz >shunit2-2.0.0.tgz.md5</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">$ gpg --default-key kate.ward@forestent.com --detach-sign shunit2-2.0.0.tgz</span>
</pre>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext"></span>
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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">UPDATE WEBSITE</span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext"></span>
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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">Again, pretty self-explainatory. Make sure to copy the MD5 and GPG signature</span>
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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">files. Once that is done, make sure to tag the website so we can go back in</span>
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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">time if needed.</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="plaintext"></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="plaintext">$ pwd</span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext">.../shunit2</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="plaintext">$ ls</span>
</pre>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext">source website</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="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="plaintext">$ svn cp -m "Release 2.0.0" \</span>
</pre>
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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">
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="plaintext">website https://shunit2.svn.sourceforge.net/svnroot/shunit2/tags/website/20060916</span>
</pre>
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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="plaintext"></span>
</pre>
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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">
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext">Now, update the website. It too is held in Subversion, so ssh into SourceForge</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">and use 'svn up' to grab the latest version.</span>
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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">
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="127" style="width: 35px; color: rgba(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="LC127" class="line" lang="plaintext">POST TO SOURCEFORGE AND FRESHMEAT</span>
</pre>
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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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<pre style="margin: 0;">+<span id="LC128" class="line" lang="plaintext"></span>
</pre>
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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">
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="plaintext">http://sourceforge.net/projects/shunit2/</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="130" style="width: 35px; color: rgba(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="LC130" class="line" lang="plaintext">http://freshmeat.net/</span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="132" style="width: 35px; color: rgba(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="LC132" class="line" lang="plaintext">#------------------------------------------------------------------------------</span>
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<td class="diff-line-num new new_line" data-linenumber="133" style="width: 35px; color: rgba(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="LC133" class="line" lang="plaintext"># Related documentation</span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext">#</span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="plaintext">Docbook XML</span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="plaintext"> docbook-xml-4.4.zip</span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="plaintext"> http://www.docbook.org/xml/4.4/docbook-xml-4.4.zip</span>
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="plaintext"> http://www.oasis-open.org/docbook/xml/4.4/docbook-xml-4.4.zip</span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="plaintext"> docbook-xml-4.5.zip</span>
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="plaintext"> http://www.docbook.org/xml/4.5/docbook-xml-4.5.zip</span>
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="plaintext">Docbook XSL</span>
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="plaintext"> docbook-xsl-1.71.0.tar.bz2</span>
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="plaintext"> http://prdownloads.sourceforge.net/docbook/docbook-xsl-1.71.0.tar.bz2?download</span>
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="plaintext"> docbook-xsl-1.71.1.tar.bz2</span>
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="plaintext"> http://downloads.sourceforge.net/docbook/docbook-xsl-1.71.1.tar.bz2?use_mirror=puzzle</span>
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="plaintext">JUnit</span>
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="plaintext"> http://www.junit.org</span>
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="plaintext"></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="plaintext">$Revision$</span></pre>
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</li>
<li id="98008977d0dfe0f09f9aff8917398596efa768c4">
<a href="https://salsa.debian.org/med-team/sambamba/commit/22dc4a7940dc5de9eada1184d972cdcab89ba973#98008977d0dfe0f09f9aff8917398596efa768c4"><strong>contrib/shunit2-2.0.3/contributors.txt</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">The original author of shunit2 is Kate Ward. The following people have</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">contributed in some way or another to shunit2.</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Bryan Larsen</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">Kevin Van Horn</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Mathias Goldau</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Richard Jensen</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">Rob Holland</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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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">$Revision$</span></pre>
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<a href="https://salsa.debian.org/med-team/sambamba/commit/22dc4a7940dc5de9eada1184d972cdcab89ba973#fa645edeaa751e7af75579bbf93d43bfef0c9ef8"><strong>contrib/shunit2-2.0.3/shunit2</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;"># $Id$</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># vim:syntax=sh:sts=2</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># vim:foldmethod=marker:foldmarker=/**,*/</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#/**</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <?xml version="1.0" encoding="UTF-8"?></span></span>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <s:shelldoc xmlns:s="http://www.forestent.com/projects/shelldoc/xsl/2005.0"></span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <s:header></span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># shUnit 2.0.4</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;"># Shell Unit Test Framework</span></span>
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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="shell"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># http://code.google.com/p/shunit2/</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># written by Kate Ward <kate.ward@forestent.com></span></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="shell"><span class="c" style="color: #998; font-style: italic;"># released under the LGPL</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># this module implements a xUnit based unit test framework similar to JUnit</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </s:header></span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#*/</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># shell flags for shunit:</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># u - treat unset variables as an error when performing parameter expansion</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"><span class="nv" style="color: teal;">__SHUNIT_SHELL_FLAGS</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">'u'</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># save the current set of shell flags, and then set some for ourselves</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"><span class="nv" style="color: teal;">__shunit_oldShellFlags</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$-</span><span class="s2" style="color: #d14;">"</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>_shunit_shellFlag <span class="k" style="font-weight: 600;">in</span> <span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">__SHUNIT_SHELL_FLAGS</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> |sed <span class="s1" style="color: #d14;">'s/\(.\)/\1 /g'</span><span class="sb" style="color: #d14;">`</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"><span class="k" style="font-weight: 600;">do</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">set</span> -<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">_shunit_shellFlag</span><span class="k" style="font-weight: 600;">}</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell"><span class="nb" style="color: #0086b3;">unset </span>_shunit_shellFlag</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># constants</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell"><span class="nv" style="color: teal;">__SHUNIT_VERSION</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">'2.0.4pre'</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell"><span class="nv" style="color: teal;">__SHUNIT_TRUE</span><span class="o" style="font-weight: 600;">=</span>0</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="shell"><span class="nv" style="color: teal;">__SHUNIT_FALSE</span><span class="o" style="font-weight: 600;">=</span>1</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="shell"><span class="nv" style="color: teal;">__SHUNIT_ERROR</span><span class="o" style="font-weight: 600;">=</span>2</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="shell"><span class="nv" style="color: teal;">__SHUNIT_ASSERT_MSG_PREFIX</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">'ASSERT:'</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>_su_const <span class="k" style="font-weight: 600;">in</span> <span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">set</span> |grep <span class="s2" style="color: #d14;">"^__SHUNIT_"</span> |cut <span class="nt" style="color: navy;">-d</span><span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: navy;">-f1</span><span class="sb" style="color: #d14;">`</span><span class="p">;</span> <span class="k" style="font-weight: 600;">do</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">readonly</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">_su_const</span><span class="k" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="shell"><span class="nb" style="color: #0086b3;">unset </span>_su_const</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># variables</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="shell"><span class="nv" style="color: teal;">__shunit_suite</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">''</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="shell"><span class="nv" style="color: teal;">__shunit_testsPassed</span><span class="o" style="font-weight: 600;">=</span>0</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="shell"><span class="nv" style="color: teal;">__shunit_testsFailed</span><span class="o" style="font-weight: 600;">=</span>0</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="shell"><span class="nv" style="color: teal;">__shunit_testsTotal</span><span class="o" style="font-weight: 600;">=</span>0</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#-----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># assert functions</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#/**</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <s:function group="asserts"></span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <entry align="right"></span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <emphasis>void</emphasis></span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </entry></span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <entry></span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <funcsynopsis></span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <funcprototype></span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <funcdef><function>assertEquals</function></funcdef></span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <paramdef>string <parameter>[message]</parameter></paramdef></span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <paramdef>string <parameter>expected</parameter></paramdef></span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <paramdef>string <parameter>actual</parameter></paramdef></span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </funcprototype></span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </funcsynopsis></span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <para>Asserts that <emphasis>expected</emphasis> and</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <emphasis>actual</emphasis> are equal to one another. The message is</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># optional.</para></span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </entry></span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </s:function></span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#*/</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="shell">assertEquals<span class="o" style="font-weight: 600;">()</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="shell"><span class="o" style="font-weight: 600;">{</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="shell"> <span class="nv" style="color: teal;">_su_message</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">''</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: teal;">$# </span><span class="nt" style="color: navy;">-eq</span> 3 <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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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: teal;">_su_message</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">$1</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">shift</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="shell"><span class="nb" style="color: #0086b3;"> </span><span class="k" style="font-weight: 600;">fi</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: teal;">_su_expected</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">1</span><span class="k" style="font-weight: 600;">:-}</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="shell"> <span class="nv" style="color: teal;">_su_actual</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">2</span><span class="k" style="font-weight: 600;">:-}</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="shell"></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="shell"> <span class="nv" style="color: teal;">shunit_return</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">__SHUNIT_TRUE</span><span class="k" style="font-weight: 600;">}</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" 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;">${</span><span class="nv" style="color: teal;">_su_expected</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">_su_actual</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="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>_shunit_testPassed</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="shell"> <span class="k" style="font-weight: 600;">else</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>failNotEquals <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">_su_message</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">_su_expected</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">_su_actual</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="shell"> <span class="nv" style="color: teal;">shunit_return</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">__SHUNIT_FALSE</span><span class="k" style="font-weight: 600;">}</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="shell"></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">unset </span>_su_message _su_expected _su_actual</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="shell"> <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">shunit_return</span><span class="k" style="font-weight: 600;">}</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="shell"></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#/**</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <s:function group="asserts"></span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <entry align="right"></span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <emphasis>void</emphasis></span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </entry></span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <entry></span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <funcsynopsis></span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <funcprototype></span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <funcdef><function>assertNull</function></funcdef></span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <paramdef>string <parameter>[message]</parameter></paramdef></span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <paramdef>string <parameter>value</parameter></paramdef></span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </funcprototype></span></span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </funcsynopsis></span></span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <para>Asserts that <emphasis>value</emphasis> is <literal>null</literal>,</span></span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># or in shell terms a zero-length string. The message is optional.</para></span></span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </entry></span></span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </s:function></span></span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#*/</span></span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="shell">assertNull<span class="o" style="font-weight: 600;">()</span></span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="shell"><span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: teal;">$# </span><span class="nt" style="color: navy;">-eq</span> 2 <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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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>assertTrue <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$1</span><span class="s2" style="color: #d14;">"</span> <span class="s2" style="color: #d14;">"[ -z '</span><span class="nv" style="color: teal;">$2</span><span class="s2" style="color: #d14;">' ]"</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="shell"> <span class="k" style="font-weight: 600;">else</span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>assertTrue <span class="s2" style="color: #d14;">"[ -z '</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">1</span><span class="k" style="font-weight: 600;">:-}</span><span class="s2" style="color: #d14;">' ]"</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#/**</span></span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <s:function group="asserts"></span></span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <entry align="right"></span></span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <emphasis>void</emphasis></span></span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </entry></span></span>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <entry></span></span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <funcsynopsis></span></span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <funcprototype></span></span>
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <funcdef><function>assertNotNull</function></funcdef></span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <paramdef>string <parameter>[message]</parameter></paramdef></span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <paramdef>string <parameter>value</parameter></paramdef></span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </funcprototype></span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </funcsynopsis></span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <para>Asserts that <emphasis>value</emphasis> is <emphasis</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># role="strong">not</emphasis> <literal>null</literal>, or in shell terms not</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># a zero-length string. The message is optional.</para></span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </entry></span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </s:function></span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#*/</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="shell">assertNotNull<span class="o" style="font-weight: 600;">()</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="shell"><span class="o" style="font-weight: 600;">{</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: teal;">$# </span><span class="nt" style="color: navy;">-eq</span> 2 <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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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>assertTrue <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$1</span><span class="s2" style="color: #d14;">"</span> <span class="s2" style="color: #d14;">"[ -n '</span><span class="nv" style="color: teal;">$2</span><span class="s2" style="color: #d14;">' ]"</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="shell"> <span class="k" style="font-weight: 600;">else</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>assertTrue <span class="s2" style="color: #d14;">"[ -n '</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">1</span><span class="k" style="font-weight: 600;">:-}</span><span class="s2" style="color: #d14;">' ]"</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="shell"></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#/**</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <s:function group="asserts"></span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <entry align="right"></span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <emphasis>void</emphasis></span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </entry></span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <entry></span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <funcsynopsis></span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <funcprototype></span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <funcdef><function>assertSame</function></funcdef></span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <paramdef>string <parameter>[message]</parameter></paramdef></span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <paramdef>string <parameter>expected</parameter></paramdef></span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <paramdef>string <parameter>actual</parameter></paramdef></span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </funcprototype></span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </funcsynopsis></span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <para>This function is functionally equivalent to</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <function>assertEquals</function>.</para></span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </entry></span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </s:function></span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#*/</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="shell">assertSame<span class="o" style="font-weight: 600;">()</span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="shell"><span class="o" style="font-weight: 600;">{</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="shell"> assertEquals <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="p">@</span><span class="k" style="font-weight: 600;">:-}</span><span class="s2" style="color: #d14;">"</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="shell"></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#/**</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <s:function group="asserts"></span></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <entry align="right"></span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <emphasis>void</emphasis></span></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </entry></span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <entry></span></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <funcsynopsis></span></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <funcprototype></span></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <funcdef><function>assertNotSame</function></funcdef></span></span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <paramdef>string <parameter>[message]</parameter></paramdef></span></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <paramdef>string <parameter>unexpected</parameter></paramdef></span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <paramdef>string <parameter>actual</parameter></paramdef></span></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </funcprototype></span></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </funcsynopsis></span></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <para>Asserts that <emphasis>unexpected</emphasis> and</span></span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <emphasis>actual</emphasis> are <emphasis role="strong">not</emphasis></span></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># equal to one another. The message is optional.</para></span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </entry></span></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </s:function></span></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#*/</span></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="shell">assertNotSame<span class="o" style="font-weight: 600;">()</span></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="shell"><span class="o" style="font-weight: 600;">{</span></span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="shell"> <span class="nv" style="color: teal;">_su_message</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">''</span></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: teal;">$# </span><span class="nt" style="color: navy;">-eq</span> 3 <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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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: teal;">_su_message</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">$1</span></span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">shift</span></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="shell"><span class="nb" style="color: #0086b3;"> </span><span class="k" style="font-weight: 600;">fi</span></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: teal;">_su_unexpected</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">1</span><span class="k" style="font-weight: 600;">:-}</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="shell"> <span class="nv" style="color: teal;">_su_actual</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">2</span><span class="k" style="font-weight: 600;">:-}</span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="shell"></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="shell"> <span class="nv" style="color: teal;">shunit_return</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">__SHUNIT_TRUE</span><span class="k" style="font-weight: 600;">}</span></span>
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211
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<pre style="margin: 0;">+<span id="LC211" 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;">${</span><span class="nv" style="color: teal;">_su_unexpected</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">_su_actual</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="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>_shunit_testPassed</span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="shell"> <span class="k" style="font-weight: 600;">else</span></span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>failSame <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">_su_message</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="shell"> <span class="nv" style="color: teal;">shunit_return</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">__SHUNIT_FALSE</span><span class="k" style="font-weight: 600;">}</span></span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="shell"></span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">unset </span>_su_message _su_unexpected _su_actual</span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="shell"> <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">shunit_return</span><span class="k" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#/**</span></span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <s:function group="asserts"></span></span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <entry align="right"></span></span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <emphasis>void</emphasis></span></span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </entry></span></span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <entry></span></span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <funcsynopsis></span></span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <funcprototype></span></span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <funcdef><function>assertTrue</function></funcdef></span></span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <paramdef>string <parameter>[message]</parameter></paramdef></span></span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <paramdef>string <parameter>condition</parameter></paramdef></span></span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </funcprototype></span></span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </funcsynopsis></span></span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <para>Asserts that a given shell test condition is true. The message is</span></span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># optional.</para></span></span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <para>Testing whether something is true or false is easy enough by using</span></span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># the assertEquals/assertNotSame functions. Shell supports much more</span></span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># complicated tests though, and a means to support them was needed. As such,</span></span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># this function tests that conditions are true or false through evaluation</span></span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># rather than just looking for a true or false.</para></span></span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <funcsynopsis></span></span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># The following test will succeed: <funcsynopsisinfo>assertTrue "[ 34 -gt 23 ]"</funcsynopsisinfo></span></span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># The following test will fail with a message: <funcsynopsisinfo>assertTrue "test failed" "[ -r '/non/existent/file' ]"</funcsynopsisinfo></span></span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </funcsynopsis></span></span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </entry></span></span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </s:function></span></span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#*/</span></span>
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="shell">assertTrue<span class="o" style="font-weight: 600;">()</span></span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="shell"><span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="shell"> <span class="nv" style="color: teal;">_su_message</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">''</span></span>
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: teal;">$# </span><span class="nt" style="color: navy;">-eq</span> 2 <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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<pre style="margin: 0;">+<span id="LC253" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: teal;">_su_message</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">$1</span></span>
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">shift</span></span>
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255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="shell"><span class="nb" style="color: #0086b3;"> </span><span class="k" style="font-weight: 600;">fi</span></span>
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256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: teal;">_su_condition</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">1</span><span class="k" style="font-weight: 600;">:-}</span></span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="shell"></span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="shell"> <span class="nv" style="color: teal;">shunit_return</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">__SHUNIT_TRUE</span><span class="k" style="font-weight: 600;">}</span></span>
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259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="shell"></span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># see if condition is an integer, i.e. a return value</span></span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="shell"> <span class="nv" style="color: teal;">_su_match</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">expr</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">_su_condition</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> : <span class="s1" style="color: #d14;">'\([0-9]*\)'</span><span class="sb" style="color: #d14;">`</span></span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-z</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">_su_condition</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># null condition</span></span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="shell"> <span class="nv" style="color: teal;">shunit_return</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">__SHUNIT_FALSE</span><span class="k" style="font-weight: 600;">}</span></span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="shell"> <span class="k" style="font-weight: 600;">elif</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">_su_condition</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">_su_match</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="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># possible return value. treating 0 as true, and non-zero as false.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="shell"> <span class="o" style="font-weight: 600;">[</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">_su_condition</span><span class="k" style="font-weight: 600;">}</span> <span class="nt" style="color: navy;">-ne</span> 0 <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: teal;">shunit_return</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">__SHUNIT_FALSE</span><span class="k" style="font-weight: 600;">}</span></span>
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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="shell"> <span class="k" style="font-weight: 600;">else</span></span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># (hopefully) a condition</span></span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="shell"> <span class="o" style="font-weight: 600;">(</span> <span class="nb" style="color: #0086b3;">eval</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">_su_condition</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">></span>/dev/null 2>&1</span>
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="shell"> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: teal;">$?</span> <span class="nt" style="color: navy;">-ne</span> 0 <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: teal;">shunit_return</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">__SHUNIT_FALSE</span><span class="k" style="font-weight: 600;">}</span></span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># record the test</span></span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">shunit_return</span><span class="k" style="font-weight: 600;">}</span> <span class="nt" style="color: navy;">-eq</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">__SHUNIT_TRUE</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>_shunit_testPassed</span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="shell"> <span class="k" style="font-weight: 600;">else</span></span>
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278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>_shunit_testFailed <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">_su_message</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="shell"></span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">unset </span>_su_message _su_condition _su_match</span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="shell"> <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">shunit_return</span><span class="k" style="font-weight: 600;">}</span></span>
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="shell"></span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#/**</span></span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <s:function group="asserts"></span></span>
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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <entry align="right"></span></span>
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288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <emphasis>void</emphasis></span></span>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </entry></span></span>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <entry></span></span>
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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <funcsynopsis></span></span>
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292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <funcprototype></span></span>
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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <funcdef><function>assertFalse</function></funcdef></span></span>
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294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <paramdef>string <parameter>[message]</parameter></paramdef></span></span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <paramdef>string <parameter>condition</parameter></paramdef></span></span>
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </funcprototype></span></span>
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297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </funcsynopsis></span></span>
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <para>Asserts that a given shell test condition is false. The message is</span></span>
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># optional.</para></span></span>
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <para>Testing whether something is true or false is easy enough by using</span></span>
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301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># the assertEquals/assertNotSame functions. Shell supports much more</span></span>
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># complicated tests though, and a means to support them was needed. As such,</span></span>
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># this function tests that conditions are true or false through evaluation</span></span>
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># rather than just looking for a true or false.</para></span></span>
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <funcsynopsis></span></span>
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># The following test will succeed: <funcsynopsisinfo>assertFalse "[ 'apples' = 'oranges' ]"</funcsynopsisinfo></span></span>
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># The following test will fail with a message: <funcsynopsisinfo>assertFalse "test failed" "[ 1 -eq 1 -a 2 -eq 2 ]"</funcsynopsisinfo></span></span>
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </funcsynopsis></span></span>
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </entry></span></span>
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </s:function></span></span>
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#*/</span></span>
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="shell">assertFalse<span class="o" style="font-weight: 600;">()</span></span>
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="shell"><span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="shell"> <span class="nv" style="color: teal;">_su_message</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">''</span></span>
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: teal;">$# </span><span class="nt" style="color: navy;">-eq</span> 2 <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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316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: teal;">_su_message</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">$1</span></span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">shift</span></span>
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318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="shell"><span class="nb" style="color: #0086b3;"> </span><span class="k" style="font-weight: 600;">fi</span></span>
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319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: teal;">_su_condition</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">1</span><span class="k" style="font-weight: 600;">:-}</span></span>
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="shell"> <span class="nv" style="color: teal;">shunit_return</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">__SHUNIT_TRUE</span><span class="k" style="font-weight: 600;">}</span></span>
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322
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="shell"></span>
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323
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># see if condition is an integer, i.e. a return value</span></span>
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324
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="shell"> <span class="nv" style="color: teal;">_su_match</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">expr</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">_su_condition</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> : <span class="s1" style="color: #d14;">'\([0-9]*\)'</span><span class="sb" style="color: #d14;">`</span></span>
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325
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-z</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">_su_condition</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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326
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># null condition</span></span>
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327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="shell"> <span class="nv" style="color: teal;">shunit_return</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">__SHUNIT_FALSE</span><span class="k" style="font-weight: 600;">}</span></span>
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328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="shell"> <span class="k" style="font-weight: 600;">elif</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">_su_condition</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">_su_match</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="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># possible return value. treating 0 as true, and non-zero as false.</span></span>
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330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="shell"> <span class="o" style="font-weight: 600;">[</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">_su_condition</span><span class="k" style="font-weight: 600;">}</span> <span class="nt" style="color: navy;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: teal;">shunit_return</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">__SHUNIT_FALSE</span><span class="k" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="shell"> <span class="k" style="font-weight: 600;">else</span></span>
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332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># (hopefully) a condition</span></span>
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333
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="shell"> <span class="o" style="font-weight: 600;">(</span> <span class="nb" style="color: #0086b3;">eval</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">_su_condition</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">></span>/dev/null 2>&1</span>
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334
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="shell"> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: teal;">$?</span> <span class="nt" style="color: navy;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: teal;">shunit_return</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">__SHUNIT_FALSE</span><span class="k" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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336
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="shell"></span>
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337
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># record the test</span></span>
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338
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">shunit_return</span><span class="k" style="font-weight: 600;">}</span> <span class="nt" style="color: navy;">-eq</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">__SHUNIT_TRUE</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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339
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>_shunit_testPassed</span>
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340
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="shell"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>_shunit_testFailed <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">_su_message</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">unset </span>_su_message _su_condition _su_match</span>
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="shell"> <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">shunit_return</span><span class="k" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#-----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># failure functions</span></span>
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#/**</span></span>
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <s:function group="failures"></span></span>
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <entry align="right"></span></span>
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <emphasis>void</emphasis></span></span>
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </entry></span></span>
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <entry></span></span>
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358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <funcsynopsis></span></span>
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359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <funcprototype></span></span>
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <funcdef><function>fail</function></funcdef></span></span>
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361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <paramdef>string <parameter>[message]</parameter></paramdef></span></span>
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362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </funcprototype></span></span>
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363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </funcsynopsis></span></span>
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364
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <para>Fails the test immediately, with the optional message.</para></span></span>
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365
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </entry></span></span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </s:function></span></span>
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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#*/</span></span>
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368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="shell">fail<span class="o" style="font-weight: 600;">()</span></span>
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369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="shell"><span class="o" style="font-weight: 600;">{</span></span>
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370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="shell"> <span class="nv" style="color: teal;">_su_message</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">1</span><span class="k" style="font-weight: 600;">:-}</span></span>
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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="shell"></span>
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372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="shell"> _shunit_testFailed <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">_su_message</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="shell"></span>
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374
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">unset </span>_su_message</span>
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375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="shell"></span>
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377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#/**</span></span>
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378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <s:function group="failures"></span></span>
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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <entry align="right"></span></span>
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380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <emphasis>void</emphasis></span></span>
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381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </entry></span></span>
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382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <entry></span></span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <funcsynopsis></span></span>
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384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <funcprototype></span></span>
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385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <funcdef><function>failNotEquals</function></funcdef></span></span>
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386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <paramdef>string <parameter>[message]</parameter></paramdef></span></span>
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387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <paramdef>string <parameter>unexpected</parameter></paramdef></span></span>
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388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <paramdef>string <parameter>actual</parameter></paramdef></span></span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </funcprototype></span></span>
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </funcsynopsis></span></span>
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <para>Fails the test if <emphasis>unexpected</emphasis> and</span></span>
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392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <emphasis>actual</emphasis> are <emphasis role="strong">not</emphasis></span></span>
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># equal to one another. The message is optional.</para></span></span>
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </entry></span></span>
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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </s:function></span></span>
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#*/</span></span>
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="shell">failNotEquals<span class="o" style="font-weight: 600;">()</span></span>
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398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="shell"><span class="o" style="font-weight: 600;">{</span></span>
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399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="shell"> <span class="nv" style="color: teal;">_su_message</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">''</span></span>
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400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: teal;">$# </span><span class="nt" style="color: navy;">-eq</span> 3 <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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401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: teal;">_su_message</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">$1</span></span>
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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">shift</span></span>
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403
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="shell"><span class="nb" style="color: #0086b3;"> </span><span class="k" style="font-weight: 600;">fi</span></span>
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404
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: teal;">_su_unexpected</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">1</span><span class="k" style="font-weight: 600;">:-}</span></span>
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405
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="shell"> <span class="nv" style="color: teal;">_su_actual</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">2</span><span class="k" style="font-weight: 600;">:-}</span></span>
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406
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="shell"></span>
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407
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="shell"> _shunit_testFailed <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">_su_message</span>:+<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">_su_message</span><span class="k" style="font-weight: 600;">}</span><span class="p"> </span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">expected:<</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">_su_unexpected</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">> but was:<</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">_su_actual</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">>"</span></span>
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408
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="shell"></span>
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409
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">unset </span>_su_message _su_unexpected _su_actual</span>
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410
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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411
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="shell"></span>
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412
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#/**</span></span>
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <s:function group="failures"></span></span>
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414
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <entry align="right"></span></span>
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415
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <emphasis>void</emphasis></span></span>
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </entry></span></span>
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417
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <entry></span></span>
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418
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <funcsynopsis></span></span>
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419
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <funcprototype></span></span>
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <funcdef><function>failSame</function></funcdef></span></span>
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421
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <paramdef>string <parameter>[message]</parameter></paramdef></span></span>
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422
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </funcprototype></span></span>
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423
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </funcsynopsis></span></span>
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <para>Indicate test failure because arguments were not the same. The</span></span>
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425
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># message is optional.</para></span></span>
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </entry></span></span>
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </s:function></span></span>
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#*/</span></span>
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="shell">failSame<span class="o" style="font-weight: 600;">()</span></span>
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430
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="shell"><span class="o" style="font-weight: 600;">{</span></span>
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431
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="shell"> <span class="nv" style="color: teal;">_su_message</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">1</span><span class="k" style="font-weight: 600;">:-}</span></span>
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432
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="shell"></span>
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433
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="shell"> _shunit_testFailed <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">_su_message</span>:+<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">_su_message</span><span class="k" style="font-weight: 600;">}</span><span class="p"> </span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">expected not same"</span></span>
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434
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="shell"></span>
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435
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">unset </span>_su_message</span>
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436
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#/**</span></span>
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <s:function group="failures"></span></span>
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <entry align="right"></span></span>
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <emphasis>void</emphasis></span></span>
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442
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </entry></span></span>
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <entry></span></span>
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <funcsynopsis></span></span>
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <funcprototype></span></span>
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <funcdef><function>failNotSame</function></funcdef></span></span>
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <paramdef>string <parameter>[message]</parameter></paramdef></span></span>
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448
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <paramdef>string <parameter>expected</parameter></paramdef></span></span>
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <paramdef>string <parameter>actual</parameter></paramdef></span></span>
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </funcprototype></span></span>
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451
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </funcsynopsis></span></span>
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <para>Fails the test if <emphasis>expected</emphasis> and</span></span>
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <emphasis>actual</emphasis> are equal to one another. The message is</span></span>
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># optional.</para></span></span>
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </entry></span></span>
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </s:function></span></span>
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#*/</span></span>
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="shell">failNotSame<span class="o" style="font-weight: 600;">()</span></span>
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459
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="shell"><span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="shell"> failNotEquals <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="p">@</span><span class="k" style="font-weight: 600;">:-}</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#-----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">+<span id="LC464" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># suite functions</span></span>
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#/**</span></span>
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <s:function group="suites"></span></span>
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <entry align="right"></span></span>
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <emphasis>void</emphasis></span></span>
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </entry></span></span>
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <entry></span></span>
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <funcsynopsis></span></span>
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<pre style="margin: 0;">+<span id="LC474" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <funcprototype></span></span>
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <funcdef><function>suite</function></funcdef></span></span>
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <paramdef /></span></span>
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </funcprototype></span></span>
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478
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </funcsynopsis></span></span>
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <para>This function can be optionally overridden by the user in their test</span></span>
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480
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># suite.</para></span></span>
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481
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <para>If this function exists, it will be called when</span></span>
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482
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <command>shunit2</command> is sourced. If it does not exist, shUnit2 will</span></span>
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483
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<pre style="margin: 0;">+<span id="LC483" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># search the parent script for all functions beginning with the word</span></span>
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484
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <literal>test</literal>, and they will be added dynamically to the test</span></span>
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485
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># suite.</para></span></span>
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486
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </entry></span></span>
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487
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </s:function></span></span>
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488
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#*/</span></span>
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489
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Note: see _shunit_mktempFunc() for actual implementation</span></span>
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490
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># suite() { :; }</span></span>
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491
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="shell"></span>
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492
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#/**</span></span>
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493
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <s:function group="suites"></span></span>
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494
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <entry align="right"></span></span>
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495
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <emphasis>void</emphasis></span></span>
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496
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </entry></span></span>
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497
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <entry></span></span>
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498
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <funcsynopsis></span></span>
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499
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <funcprototype></span></span>
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500
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <funcdef><function>suite_addTest</function></funcdef></span></span>
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501
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <paramdef>string <parameter>function</parameter></paramdef></span></span>
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502
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </funcprototype></span></span>
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503
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </funcsynopsis></span></span>
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504
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<pre style="margin: 0;">+<span id="LC504" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <para>This function adds a function name to the list of tests scheduled for</span></span>
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505
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<pre style="margin: 0;">+<span id="LC505" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># execution as part of this test suite. This function should only be called</span></span>
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506
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<pre style="margin: 0;">+<span id="LC506" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># from within the <function>suite()</function> function.</para></span></span>
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507
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </entry></span></span>
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508
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<pre style="margin: 0;">+<span id="LC508" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </s:function></span></span>
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<pre style="margin: 0;">+<span id="LC509" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#*/</span></span>
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<pre style="margin: 0;">+<span id="LC510" class="line" lang="shell">suite_addTest<span class="o" style="font-weight: 600;">()</span></span>
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="shell"><span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="shell"> <span class="nv" style="color: teal;">_su_func</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">1</span><span class="k" style="font-weight: 600;">:-}</span></span>
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513
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<pre style="margin: 0;">+<span id="LC513" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC514" class="line" lang="shell"> <span class="nv" style="color: teal;">__shunit_suite</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">__shunit_suite</span>:+<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">__shunit_suite</span><span class="k" style="font-weight: 600;">}</span><span class="p"> </span><span class="k" style="font-weight: 600;">}${</span><span class="nv" style="color: teal;">_su_func</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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515
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="shell"></span>
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516
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">unset </span>_su_func</span>
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517
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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518
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="shell"></span>
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519
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#/**</span></span>
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <s:function group="suites"></span></span>
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <entry align="right"></span></span>
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <emphasis>void</emphasis></span></span>
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523
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<pre style="margin: 0;">+<span id="LC523" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </entry></span></span>
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524
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<pre style="margin: 0;">+<span id="LC524" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <entry></span></span>
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525
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<pre style="margin: 0;">+<span id="LC525" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <funcsynopsis></span></span>
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526
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <funcprototype></span></span>
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527
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<pre style="margin: 0;">+<span id="LC527" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <funcdef><function>oneTimeSetUp</function></funcdef></span></span>
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528
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<pre style="margin: 0;">+<span id="LC528" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <paramdef /></span></span>
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529
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<pre style="margin: 0;">+<span id="LC529" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </funcprototype></span></span>
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530
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<pre style="margin: 0;">+<span id="LC530" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </funcsynopsis></span></span>
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531
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<pre style="margin: 0;">+<span id="LC531" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <para>This function can be be optionally overridden by the user in their</span></span>
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532
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<pre style="margin: 0;">+<span id="LC532" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># test suite.</para></span></span>
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<pre style="margin: 0;">+<span id="LC533" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <para>If this function exists, it will be called once before any tests are</span></span>
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<pre style="margin: 0;">+<span id="LC534" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># run. It is useful to prepare a common environment for all tests.</para></span></span>
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535
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<pre style="margin: 0;">+<span id="LC535" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </entry></span></span>
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<pre style="margin: 0;">+<span id="LC536" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </s:function></span></span>
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537
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#*/</span></span>
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538
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<pre style="margin: 0;">+<span id="LC538" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Note: see _shunit_mktempFunc() for actual implementation</span></span>
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539
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<pre style="margin: 0;">+<span id="LC539" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># oneTimeSetUp() { :; }</span></span>
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540
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<pre style="margin: 0;">+<span id="LC540" class="line" lang="shell"></span>
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541
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<pre style="margin: 0;">+<span id="LC541" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#/**</span></span>
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542
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<pre style="margin: 0;">+<span id="LC542" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <s:function group="suites"></span></span>
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543
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<pre style="margin: 0;">+<span id="LC543" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <entry align="right"></span></span>
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<pre style="margin: 0;">+<span id="LC544" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <emphasis>void</emphasis></span></span>
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </entry></span></span>
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <entry></span></span>
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<pre style="margin: 0;">+<span id="LC547" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <funcsynopsis></span></span>
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548
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<pre style="margin: 0;">+<span id="LC548" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <funcprototype></span></span>
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <funcdef><function>oneTimeTearDown</function></funcdef></span></span>
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550
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<pre style="margin: 0;">+<span id="LC550" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <paramdef /></span></span>
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551
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<pre style="margin: 0;">+<span id="LC551" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </funcprototype></span></span>
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552
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<pre style="margin: 0;">+<span id="LC552" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </funcsynopsis></span></span>
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553
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<pre style="margin: 0;">+<span id="LC553" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <para>This function can be be optionally overridden by the user in their</span></span>
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554
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<pre style="margin: 0;">+<span id="LC554" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># test suite.</para></span></span>
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<pre style="margin: 0;">+<span id="LC555" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <para>If this function exists, it will be called once after all tests are</span></span>
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556
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<pre style="margin: 0;">+<span id="LC556" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># completed. It is useful to clean up the environment after all tests.</para></span></span>
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557
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<pre style="margin: 0;">+<span id="LC557" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </entry></span></span>
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558
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<pre style="margin: 0;">+<span id="LC558" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </s:function></span></span>
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559
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#*/</span></span>
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560
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<pre style="margin: 0;">+<span id="LC560" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Note: see _shunit_mktempFunc() for actual implementation</span></span>
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561
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<pre style="margin: 0;">+<span id="LC561" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># oneTimeTearDown() { :; }</span></span>
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562
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="shell"></span>
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563
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<pre style="margin: 0;">+<span id="LC563" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#/**</span></span>
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564
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<pre style="margin: 0;">+<span id="LC564" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <s:function group="suites"></span></span>
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565
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<pre style="margin: 0;">+<span id="LC565" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <entry align="right"></span></span>
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566
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <emphasis>void</emphasis></span></span>
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567
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<pre style="margin: 0;">+<span id="LC567" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </entry></span></span>
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568
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<pre style="margin: 0;">+<span id="LC568" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <entry></span></span>
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569
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<pre style="margin: 0;">+<span id="LC569" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <funcsynopsis></span></span>
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570
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<pre style="margin: 0;">+<span id="LC570" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <funcprototype></span></span>
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571
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<pre style="margin: 0;">+<span id="LC571" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <funcdef><function>setUp</function></funcdef></span></span>
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572
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<pre style="margin: 0;">+<span id="LC572" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <paramdef /></span></span>
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573
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<pre style="margin: 0;">+<span id="LC573" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </funcprototype></span></span>
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574
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<pre style="margin: 0;">+<span id="LC574" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </funcsynopsis></span></span>
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575
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<pre style="margin: 0;">+<span id="LC575" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <para>This function can be be optionally overridden by the user in their</span></span>
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576
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<pre style="margin: 0;">+<span id="LC576" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># test suite.</para></span></span>
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577
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<pre style="margin: 0;">+<span id="LC577" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <para>If this function exists, it will be called before each test is run.</span></span>
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578
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<pre style="margin: 0;">+<span id="LC578" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># It is useful to reset the environment before each test.</para></span></span>
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579
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<pre style="margin: 0;">+<span id="LC579" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </entry></span></span>
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580
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<pre style="margin: 0;">+<span id="LC580" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </s:function></span></span>
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581
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<pre style="margin: 0;">+<span id="LC581" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#*/</span></span>
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582
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<pre style="margin: 0;">+<span id="LC582" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Note: see _shunit_mktempFunc() for actual implementation</span></span>
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583
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<pre style="margin: 0;">+<span id="LC583" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># setUp() { :; }</span></span>
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584
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<pre style="margin: 0;">+<span id="LC584" class="line" lang="shell"></span>
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585
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<pre style="margin: 0;">+<span id="LC585" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#/**</span></span>
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586
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<pre style="margin: 0;">+<span id="LC586" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <s:function group="suites"></span></span>
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587
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<pre style="margin: 0;">+<span id="LC587" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <entry align="right"></span></span>
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588
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<pre style="margin: 0;">+<span id="LC588" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <emphasis>void</emphasis></span></span>
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589
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<pre style="margin: 0;">+<span id="LC589" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </entry></span></span>
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590
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<pre style="margin: 0;">+<span id="LC590" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <entry></span></span>
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591
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<pre style="margin: 0;">+<span id="LC591" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <funcsynopsis></span></span>
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592
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<pre style="margin: 0;">+<span id="LC592" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <funcprototype></span></span>
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593
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<pre style="margin: 0;">+<span id="LC593" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <funcdef><function>tearDown</function></funcdef></span></span>
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594
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<pre style="margin: 0;">+<span id="LC594" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <paramdef /></span></span>
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595
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<pre style="margin: 0;">+<span id="LC595" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </funcprototype></span></span>
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596
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<pre style="margin: 0;">+<span id="LC596" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </funcsynopsis></span></span>
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597
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<pre style="margin: 0;">+<span id="LC597" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <para>This function can be be optionally overridden by the user in their</span></span>
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598
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<pre style="margin: 0;">+<span id="LC598" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># test suite.</para></span></span>
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599
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<pre style="margin: 0;">+<span id="LC599" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <para>If this function exists, it will be called after each test completes.</span></span>
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600
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<pre style="margin: 0;">+<span id="LC600" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># It is useful to clean up the environment after each test.</para></span></span>
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601
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<pre style="margin: 0;">+<span id="LC601" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </entry></span></span>
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602
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<pre style="margin: 0;">+<span id="LC602" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </s:function></span></span>
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603
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<pre style="margin: 0;">+<span id="LC603" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#*/</span></span>
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604
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<pre style="margin: 0;">+<span id="LC604" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Note: see _shunit_mktempFunc() for actual implementation</span></span>
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605
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<pre style="margin: 0;">+<span id="LC605" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># tearDown() { :; }</span></span>
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606
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<pre style="margin: 0;">+<span id="LC606" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC607" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#------------------------------------------------------------------------------</span></span>
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608
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<pre style="margin: 0;">+<span id="LC608" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># internal shUnit2 functions</span></span>
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609
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<pre style="margin: 0;">+<span id="LC609" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC610" class="line" lang="shell"></span>
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611
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<pre style="margin: 0;">+<span id="LC611" class="line" lang="shell">_shunit_cleanup<span class="o" style="font-weight: 600;">()</span></span>
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612
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<pre style="margin: 0;">+<span id="LC612" class="line" lang="shell"><span class="o" style="font-weight: 600;">{</span></span>
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613
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<pre style="margin: 0;">+<span id="LC613" class="line" lang="shell"> <span class="nv" style="color: teal;">name</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">$1</span></span>
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614
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<pre style="margin: 0;">+<span id="LC614" class="line" lang="shell"></span>
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615
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<pre style="margin: 0;">+<span id="LC615" class="line" lang="shell"> <span class="k" style="font-weight: 600;">case</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">name</span><span class="k" style="font-weight: 600;">}</span> <span class="k" style="font-weight: 600;">in</span></span>
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616
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<pre style="margin: 0;">+<span id="LC616" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>EXIT<span class="p">)</span> <span class="nv" style="color: teal;">signal</span><span class="o" style="font-weight: 600;">=</span>0 <span class="p">;;</span></span>
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617
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<pre style="margin: 0;">+<span id="LC617" class="line" lang="shell"> INT<span class="p">)</span> <span class="nv" style="color: teal;">signal</span><span class="o" style="font-weight: 600;">=</span>2 <span class="p">;;</span></span>
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618
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<pre style="margin: 0;">+<span id="LC618" class="line" lang="shell"> TERM<span class="p">)</span> <span class="nv" style="color: teal;">signal</span><span class="o" style="font-weight: 600;">=</span>15 <span class="p">;;</span></span>
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619
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<pre style="margin: 0;">+<span id="LC619" class="line" lang="shell"> <span class="k" style="font-weight: 600;">esac</span></span>
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620
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<pre style="margin: 0;">+<span id="LC620" class="line" lang="shell"></span>
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621
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<pre style="margin: 0;">+<span id="LC621" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># do our work</span></span>
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622
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<pre style="margin: 0;">+<span id="LC622" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: navy;">-fr</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">__shunit_tmpDir</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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623
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<pre style="margin: 0;">+<span id="LC623" class="line" lang="shell"></span>
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624
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<pre style="margin: 0;">+<span id="LC624" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># exit for all non-EXIT signals</span></span>
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625
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<pre style="margin: 0;">+<span id="LC625" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">name</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s1" style="color: #d14;">'EXIT'</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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626
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<pre style="margin: 0;">+<span id="LC626" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"trapped and now handling the </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">name</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;"> signal"</span> <span class="o" style="font-weight: 600;">></span>&2</span>
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627
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<pre style="margin: 0;">+<span id="LC627" class="line" lang="shell"> _shunit_generateReport</span>
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628
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<pre style="margin: 0;">+<span id="LC628" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># disable EXIT trap</span></span>
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629
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<pre style="margin: 0;">+<span id="LC629" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap </span>0</span>
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630
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<pre style="margin: 0;">+<span id="LC630" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># add 128 to signal and exit</span></span>
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631
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<pre style="margin: 0;">+<span id="LC631" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit</span> <span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">expr</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">signal</span><span class="k" style="font-weight: 600;">}</span> + 128<span class="sb" style="color: #d14;">`</span></span>
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632
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<pre style="margin: 0;">+<span id="LC632" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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633
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<pre style="margin: 0;">+<span id="LC633" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC634" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC635" class="line" lang="shell">_shunit_execSuite<span class="o" style="font-weight: 600;">()</span></span>
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<pre style="margin: 0;">+<span id="LC636" class="line" lang="shell"><span class="o" style="font-weight: 600;">{</span></span>
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637
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<pre style="margin: 0;">+<span id="LC637" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'#'</span></span>
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638
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<pre style="margin: 0;">+<span id="LC638" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'# Performing tests'</span></span>
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639
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<pre style="margin: 0;">+<span id="LC639" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'#'</span></span>
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640
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<pre style="margin: 0;">+<span id="LC640" class="line" lang="shell"> <span class="k" style="font-weight: 600;">for </span>_su_func <span class="k" style="font-weight: 600;">in</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">__shunit_suite</span><span class="k" style="font-weight: 600;">}</span><span class="p">;</span> <span class="k" style="font-weight: 600;">do</span></span>
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641
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<pre style="margin: 0;">+<span id="LC641" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># execute the per-test setup function</span></span>
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642
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<pre style="margin: 0;">+<span id="LC642" class="line" lang="shell"> setUp</span>
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643
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<pre style="margin: 0;">+<span id="LC643" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC644" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># execute the test</span></span>
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645
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<pre style="margin: 0;">+<span id="LC645" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">_su_func</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC646" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">eval</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">_su_func</span><span class="k" style="font-weight: 600;">}</span></span>
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647
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<pre style="margin: 0;">+<span id="LC647" class="line" lang="shell"></span>
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648
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<pre style="margin: 0;">+<span id="LC648" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># execute the per-test tear-down function</span></span>
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649
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<pre style="margin: 0;">+<span id="LC649" class="line" lang="shell"> tearDown</span>
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650
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<pre style="margin: 0;">+<span id="LC650" class="line" lang="shell"> <span class="k" style="font-weight: 600;">done</span></span>
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651
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<pre style="margin: 0;">+<span id="LC651" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC652" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">unset </span>_su_func</span>
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<pre style="margin: 0;">+<span id="LC653" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC654" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC655" class="line" lang="shell">_shunit_functionExists<span class="o" style="font-weight: 600;">()</span></span>
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656
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<pre style="margin: 0;">+<span id="LC656" class="line" lang="shell"><span class="o" style="font-weight: 600;">{</span></span>
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657
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<pre style="margin: 0;">+<span id="LC657" class="line" lang="shell"> <span class="nv" style="color: teal;">_su__func</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">$1</span></span>
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658
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<pre style="margin: 0;">+<span id="LC658" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">type</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">_su__func</span><span class="k" style="font-weight: 600;">}</span> 2>/dev/null |grep <span class="s2" style="color: #d14;">"is a function$"</span> <span class="o" style="font-weight: 600;">></span>/dev/null</span>
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659
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<pre style="margin: 0;">+<span id="LC659" class="line" lang="shell"> <span class="nv" style="color: teal;">_su__return</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">$?</span></span>
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660
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<pre style="margin: 0;">+<span id="LC660" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">unset </span>_su__func</span>
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<pre style="margin: 0;">+<span id="LC661" class="line" lang="shell"> <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">_su__return</span><span class="k" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC662" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC663" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC664" class="line" lang="shell">_shunit_generateReport<span class="o" style="font-weight: 600;">()</span></span>
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665
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<pre style="margin: 0;">+<span id="LC665" class="line" lang="shell"><span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC666" class="line" lang="shell"> <span class="nv" style="color: teal;">_su__awkPercent</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">'{printf("%0.0f%%", $1*100/$2)}'</span></span>
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667
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<pre style="margin: 0;">+<span id="LC667" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">__shunit_testsTotal</span><span class="k" style="font-weight: 600;">}</span> <span class="nt" style="color: navy;">-gt</span> 0 <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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668
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<pre style="margin: 0;">+<span id="LC668" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: teal;">_su__success</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">echo</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">__shunit_testsPassed</span><span class="k" style="font-weight: 600;">}</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">__shunit_testsTotal</span><span class="k" style="font-weight: 600;">}</span> |<span class="se" style="color: #d14;">\</span></span>
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669
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<pre style="margin: 0;">+<span id="LC669" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">awk</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">_su__awkPercent</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span><span class="sb" style="color: #d14;">`</span></span>
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670
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<pre style="margin: 0;">+<span id="LC670" class="line" lang="shell"> <span class="k" style="font-weight: 600;">else</span></span>
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671
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<pre style="margin: 0;">+<span id="LC671" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: teal;">_su__success</span><span class="o" style="font-weight: 600;">=</span>0</span>
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672
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<pre style="margin: 0;">+<span id="LC672" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;">+<span id="LC673" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC674" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">cat</span> <span class="o" style="font-weight: 600;"><<</span><span class="no" style="color: teal;">EOF</span></span>
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<pre style="margin: 0;">+<span id="LC676" class="line" lang="shell"><span class="sh" style="color: #d14;">#</span></span>
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<pre style="margin: 0;">+<span id="LC677" class="line" lang="shell"><span class="sh" style="color: #d14;"># Test report</span></span>
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<pre style="margin: 0;">+<span id="LC678" class="line" lang="shell"><span class="sh" style="color: #d14;">#</span></span>
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<pre style="margin: 0;">+<span id="LC679" class="line" lang="shell"><span class="sh" style="color: #d14;">tests passed: </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">__shunit_testsPassed</span><span class="k" style="font-weight: 600;">}</span></span>
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680
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<pre style="margin: 0;">+<span id="LC680" class="line" lang="shell"><span class="sh" style="color: #d14;">tests failed: </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">__shunit_testsFailed</span><span class="k" style="font-weight: 600;">}</span></span>
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681
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<pre style="margin: 0;">+<span id="LC681" class="line" lang="shell"><span class="sh" style="color: #d14;">tests total: </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">__shunit_testsTotal</span><span class="k" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC682" class="line" lang="shell"><span class="sh" style="color: #d14;">success rate: </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">_su__success</span><span class="k" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC683" class="line" lang="shell"><span class="no" style="color: teal;">EOF</span></span>
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<pre style="margin: 0;">+<span id="LC685" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">unset </span>_su__success</span>
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<pre style="margin: 0;">+<span id="LC686" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC688" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># this function is a cross-platform temporary directory creation tool. not all</span></span>
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<pre style="margin: 0;">+<span id="LC689" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># OSes have the mktemp function, so one is included here.</span></span>
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<pre style="margin: 0;">+<span id="LC690" class="line" lang="shell">_shunit_mktempDir<span class="o" style="font-weight: 600;">()</span></span>
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<pre style="margin: 0;">+<span id="LC691" class="line" lang="shell"><span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC692" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># try the standard mktemp function</span></span>
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<pre style="margin: 0;">+<span id="LC693" class="line" lang="shell"> <span class="o" style="font-weight: 600;">(</span> <span class="nb" style="color: #0086b3;">exec mktemp</span> <span class="nt" style="color: navy;">-dqt</span> shunit.XXXXXX 2>/dev/null <span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="k" style="font-weight: 600;">return</span></span>
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694
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<pre style="margin: 0;">+<span id="LC694" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC695" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># the standard mktemp didn't work. doing our own.</span></span>
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696
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<pre style="margin: 0;">+<span id="LC696" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-r</span> <span class="s1" style="color: #d14;">'/dev/urandom'</span> <span class="nt" style="color: navy;">-a</span> <span class="nt" style="color: navy;">-x</span> <span class="s1" style="color: #d14;">'/usr/bin/od'</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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<pre style="margin: 0;">+<span id="LC697" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: teal;">_su__random</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span>/usr/bin/od <span class="nt" style="color: navy;">-vAn</span> <span class="nt" style="color: navy;">-N4</span> <span class="nt" style="color: navy;">-tx4</span> </dev/urandom <span class="se" style="color: #d14;">\</span></span>
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698
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<pre style="margin: 0;">+<span id="LC698" class="line" lang="shell"> |sed <span class="s1" style="color: #d14;">'s/^[^0-9a-f]*//'</span><span class="sb" style="color: #d14;">`</span></span>
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699
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<pre style="margin: 0;">+<span id="LC699" class="line" lang="shell"> <span class="k" style="font-weight: 600;">elif</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-n</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">RANDOM</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="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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700
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<pre style="margin: 0;">+<span id="LC700" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># $RANDOM works</span></span>
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701
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<pre style="margin: 0;">+<span id="LC701" class="line" lang="shell"> <span class="nv" style="color: teal;">_su__random</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">RANDOM</span><span class="k" style="font-weight: 600;">}${</span><span class="nv" style="color: teal;">RANDOM</span><span class="k" style="font-weight: 600;">}${</span><span class="nv" style="color: teal;">RANDOM</span><span class="k" style="font-weight: 600;">}</span><span class="nv" style="color: teal;">$$</span></span>
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702
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<pre style="margin: 0;">+<span id="LC702" class="line" lang="shell"> <span class="k" style="font-weight: 600;">else</span></span>
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703
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<pre style="margin: 0;">+<span id="LC703" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># $RANDOM doesn't work</span></span>
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704
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<pre style="margin: 0;">+<span id="LC704" class="line" lang="shell"> <span class="nv" style="color: teal;">_su__date</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">date</span> <span class="s1" style="color: #d14;">'+%Y%m%d%H%M%S'</span><span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;">+<span id="LC705" class="line" lang="shell"> <span class="nv" style="color: teal;">_su__random</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">expr</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">_su__date</span><span class="k" style="font-weight: 600;">}</span> / <span class="nv" style="color: teal;">$$</span><span class="sb" style="color: #d14;">`</span></span>
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706
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<pre style="margin: 0;">+<span id="LC706" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;">+<span id="LC707" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC708" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: teal;">_su__tmpDir</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">TMPDIR</span><span class="p">-/tmp</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">/shunit.</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">_su__random</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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709
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<pre style="margin: 0;">+<span id="LC709" class="line" lang="shell"> <span class="o" style="font-weight: 600;">(</span> <span class="nb" style="color: #0086b3;">umask </span>077 <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">mkdir</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">_su__tmpDir</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">{</span></span>
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710
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<pre style="margin: 0;">+<span id="LC710" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'shUnit:FATAL could not create temporary directory! exiting'</span> <span class="o" style="font-weight: 600;">></span>&2</span>
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711
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<pre style="margin: 0;">+<span id="LC711" class="line" lang="shell"> <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">__SHUNIT_ERROR</span><span class="k" style="font-weight: 600;">}</span></span>
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712
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<pre style="margin: 0;">+<span id="LC712" class="line" lang="shell"> <span class="o" style="font-weight: 600;">}</span></span>
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713
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<pre style="margin: 0;">+<span id="LC713" class="line" lang="shell"></span>
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714
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<pre style="margin: 0;">+<span id="LC714" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">_su__tmpDir</span><span class="k" style="font-weight: 600;">}</span></span>
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715
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<pre style="margin: 0;">+<span id="LC715" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">unset </span>_su__date _su__random _su__tmpDir</span>
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716
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<pre style="margin: 0;">+<span id="LC716" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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717
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<pre style="margin: 0;">+<span id="LC717" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC718" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># this function is here to work around issues in Cygwin</span></span>
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719
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<pre style="margin: 0;">+<span id="LC719" class="line" lang="shell">_shunit_mktempFunc<span class="o" style="font-weight: 600;">()</span></span>
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720
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<pre style="margin: 0;">+<span id="LC720" class="line" lang="shell"><span class="o" style="font-weight: 600;">{</span></span>
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721
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<pre style="margin: 0;">+<span id="LC721" class="line" lang="shell"> <span class="k" style="font-weight: 600;">for </span>_su__func <span class="k" style="font-weight: 600;">in </span>oneTimeSetUp oneTimeTearDown setUp tearDown suite<span class="p">;</span> <span class="k" style="font-weight: 600;">do</span></span>
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722
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<pre style="margin: 0;">+<span id="LC722" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: teal;">_su__file</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: teal;">__shunit_tmpDir</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">/</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">_su__func</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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723
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<pre style="margin: 0;">+<span id="LC723" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">cat</span> <span class="o" style="font-weight: 600;"><<</span><span class="no" style="color: teal;">EOF</span><span class="sh" style="color: #d14;"> >"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">_su__file</span><span class="k" style="font-weight: 600;">}</span><span class="sh" style="color: #d14;">"</span></span>
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724
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<pre style="margin: 0;">+<span id="LC724" class="line" lang="shell"><span class="sh" style="color: #d14;">#! /bin/sh</span></span>
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725
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<pre style="margin: 0;">+<span id="LC725" class="line" lang="shell"><span class="sh" style="color: #d14;">exit 0</span></span>
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726
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<pre style="margin: 0;">+<span id="LC726" class="line" lang="shell"><span class="no" style="color: teal;">EOF</span></span>
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727
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<pre style="margin: 0;">+<span id="LC727" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">chmod</span> +x <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">_su__file</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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728
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<pre style="margin: 0;">+<span id="LC728" class="line" lang="shell"> <span class="k" style="font-weight: 600;">done</span></span>
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729
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<pre style="margin: 0;">+<span id="LC729" class="line" lang="shell"></span>
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730
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<pre style="margin: 0;">+<span id="LC730" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">unset </span>_su__file</span>
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731
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<pre style="margin: 0;">+<span id="LC731" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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732
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<pre style="margin: 0;">+<span id="LC732" class="line" lang="shell"></span>
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733
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<pre style="margin: 0;">+<span id="LC733" class="line" lang="shell">_shunit_testPassed<span class="o" style="font-weight: 600;">()</span></span>
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734
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<pre style="margin: 0;">+<span id="LC734" class="line" lang="shell"><span class="o" style="font-weight: 600;">{</span></span>
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735
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<pre style="margin: 0;">+<span id="LC735" class="line" lang="shell"> <span class="nv" style="color: teal;">__shunit_testsPassed</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">expr</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">__shunit_testsPassed</span><span class="k" style="font-weight: 600;">}</span> + 1<span class="sb" style="color: #d14;">`</span></span>
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736
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<pre style="margin: 0;">+<span id="LC736" class="line" lang="shell"> <span class="nv" style="color: teal;">__shunit_testsTotal</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">expr</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">__shunit_testsTotal</span><span class="k" style="font-weight: 600;">}</span> + 1<span class="sb" style="color: #d14;">`</span></span>
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737
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<pre style="margin: 0;">+<span id="LC737" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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738
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<pre style="margin: 0;">+<span id="LC738" class="line" lang="shell"></span>
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739
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<pre style="margin: 0;">+<span id="LC739" class="line" lang="shell">_shunit_testFailed<span class="o" style="font-weight: 600;">()</span></span>
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740
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<pre style="margin: 0;">+<span id="LC740" class="line" lang="shell"><span class="o" style="font-weight: 600;">{</span></span>
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741
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<pre style="margin: 0;">+<span id="LC741" class="line" lang="shell"> <span class="nv" style="color: teal;">_su__msg</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">$1</span></span>
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742
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<pre style="margin: 0;">+<span id="LC742" class="line" lang="shell"></span>
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743
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<pre style="margin: 0;">+<span id="LC743" class="line" lang="shell"> <span class="nv" style="color: teal;">__shunit_testsFailed</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">expr</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">__shunit_testsFailed</span><span class="k" style="font-weight: 600;">}</span> + 1<span class="sb" style="color: #d14;">`</span></span>
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744
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<pre style="margin: 0;">+<span id="LC744" class="line" lang="shell"> <span class="nv" style="color: teal;">__shunit_testsTotal</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">expr</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">__shunit_testsTotal</span><span class="k" style="font-weight: 600;">}</span> + 1<span class="sb" style="color: #d14;">`</span></span>
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745
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<pre style="margin: 0;">+<span id="LC745" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">__SHUNIT_ASSERT_MSG_PREFIX</span><span class="k" style="font-weight: 600;">}${</span><span class="nv" style="color: teal;">_su__msg</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">></span>&2</span>
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746
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<pre style="margin: 0;">+<span id="LC746" class="line" lang="shell"></span>
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747
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<pre style="margin: 0;">+<span id="LC747" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">unset </span>_su__msg</span>
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748
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<pre style="margin: 0;">+<span id="LC748" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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749
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<pre style="margin: 0;">+<span id="LC749" class="line" lang="shell"></span>
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750
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<pre style="margin: 0;">+<span id="LC750" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#------------------------------------------------------------------------------</span></span>
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751
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<pre style="margin: 0;">+<span id="LC751" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># main</span></span>
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<pre style="margin: 0;">+<span id="LC752" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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753
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<pre style="margin: 0;">+<span id="LC753" class="line" lang="shell"></span>
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754
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<pre style="margin: 0;">+<span id="LC754" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># create a temporary storage location</span></span>
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755
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<pre style="margin: 0;">+<span id="LC755" class="line" lang="shell"><span class="nv" style="color: teal;">__shunit_tmpDir</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span>_shunit_mktempDir<span class="sb" style="color: #d14;">`</span> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">exit</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">__SHUNIT_ERROR</span><span class="k" style="font-weight: 600;">}</span></span>
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756
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<pre style="margin: 0;">+<span id="LC756" class="line" lang="shell"></span>
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757
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<pre style="margin: 0;">+<span id="LC757" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># setup traps to clean up after ourselves</span></span>
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758
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<pre style="margin: 0;">+<span id="LC758" class="line" lang="shell"><span class="nb" style="color: #0086b3;">trap</span> <span class="s1" style="color: #d14;">'_shunit_cleanup EXIT'</span> 0</span>
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759
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<pre style="margin: 0;">+<span id="LC759" class="line" lang="shell"><span class="nb" style="color: #0086b3;">trap</span> <span class="s1" style="color: #d14;">'_shunit_cleanup INT'</span> 2</span>
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760
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<pre style="margin: 0;">+<span id="LC760" class="line" lang="shell"><span class="nb" style="color: #0086b3;">trap</span> <span class="s1" style="color: #d14;">'_shunit_cleanup TERM'</span> 15</span>
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761
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<pre style="margin: 0;">+<span id="LC761" class="line" lang="shell"></span>
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762
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<pre style="margin: 0;">+<span id="LC762" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># create phantom functions to work around issues with Cygwin</span></span>
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763
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<pre style="margin: 0;">+<span id="LC763" class="line" lang="shell">_shunit_mktempFunc</span>
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764
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<pre style="margin: 0;">+<span id="LC764" class="line" lang="shell"><span class="nv" style="color: teal;">PATH</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">__shunit_tmpDir</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">:</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">PATH</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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765
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<pre style="margin: 0;">+<span id="LC765" class="line" lang="shell"></span>
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766
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<pre style="margin: 0;">+<span id="LC766" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># execute the oneTimeSetUp function (if it exists)</span></span>
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767
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<pre style="margin: 0;">+<span id="LC767" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#_shunit_functionExists oneTimeSetUp && oneTimeSetUp</span></span>
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768
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<pre style="margin: 0;">+<span id="LC768" class="line" lang="shell">oneTimeSetUp</span>
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769
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<pre style="margin: 0;">+<span id="LC769" class="line" lang="shell"></span>
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770
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<pre style="margin: 0;">+<span id="LC770" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># deprecated: execute the suite function defined in the parent test script</span></span>
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771
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<pre style="margin: 0;">+<span id="LC771" class="line" lang="shell">suite</span>
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772
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<pre style="margin: 0;">+<span id="LC772" class="line" lang="shell"></span>
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773
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<pre style="margin: 0;">+<span id="LC773" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># if no suite function was defined, dynamically build a list of functions</span></span>
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774
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<pre style="margin: 0;">+<span id="LC774" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-z</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">__shunit_suite</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="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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775
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<pre style="margin: 0;">+<span id="LC775" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: teal;">funcs</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">grep</span> <span class="s2" style="color: #d14;">"^[ </span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">]*test[A-Za-z0-9_]* *()"</span> <span class="nv" style="color: teal;">$0</span> |sed <span class="s1" style="color: #d14;">'s/[^A-Za-z0-9_]//g'</span><span class="sb" style="color: #d14;">`</span></span>
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776
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<pre style="margin: 0;">+<span id="LC776" class="line" lang="shell"> <span class="k" style="font-weight: 600;">for </span>func <span class="k" style="font-weight: 600;">in</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">funcs</span><span class="k" style="font-weight: 600;">}</span><span class="p">;</span> <span class="k" style="font-weight: 600;">do</span></span>
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777
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<pre style="margin: 0;">+<span id="LC777" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>suite_addTest <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">func</span><span class="k" style="font-weight: 600;">}</span></span>
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778
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<pre style="margin: 0;">+<span id="LC778" class="line" lang="shell"> <span class="k" style="font-weight: 600;">done</span></span>
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779
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<pre style="margin: 0;">+<span id="LC779" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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780
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<pre style="margin: 0;">+<span id="LC780" class="line" lang="shell"></span>
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781
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<pre style="margin: 0;">+<span id="LC781" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># execute the tests</span></span>
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782
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<pre style="margin: 0;">+<span id="LC782" class="line" lang="shell">_shunit_execSuite</span>
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783
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<pre style="margin: 0;">+<span id="LC783" class="line" lang="shell"></span>
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784
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<pre style="margin: 0;">+<span id="LC784" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># execute the oneTimeTearDown function (if it exists)</span></span>
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785
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<pre style="margin: 0;">+<span id="LC785" class="line" lang="shell">oneTimeTearDown</span>
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786
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<pre style="margin: 0;">+<span id="LC786" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC787" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># generate report</span></span>
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788
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<pre style="margin: 0;">+<span id="LC788" class="line" lang="shell">_shunit_generateReport</span>
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<pre style="margin: 0;">+<span id="LC789" class="line" lang="shell"></span>
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790
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<pre style="margin: 0;">+<span id="LC790" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># restore the previous set of shell flags</span></span>
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791
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<pre style="margin: 0;">+<span id="LC791" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>_shunit_shellFlag <span class="k" style="font-weight: 600;">in</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">__SHUNIT_SHELL_FLAGS</span><span class="k" style="font-weight: 600;">}</span><span class="p">;</span> <span class="k" style="font-weight: 600;">do</span></span>
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792
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<pre style="margin: 0;">+<span id="LC792" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">__shunit_oldShellFlags</span><span class="k" style="font-weight: 600;">}</span> |grep <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">_shunit_shellFlag</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">></span>/dev/null <span class="se" style="color: #d14;">\</span></span>
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793
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<pre style="margin: 0;">+<span id="LC793" class="line" lang="shell"> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">set</span> +<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">_shunit_shellFlag</span><span class="k" style="font-weight: 600;">}</span></span>
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794
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<pre style="margin: 0;">+<span id="LC794" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span>
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795
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<pre style="margin: 0;">+<span id="LC795" class="line" lang="shell"><span class="nb" style="color: #0086b3;">unset </span>_shunit_shellFlag</span>
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796
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<pre style="margin: 0;">+<span id="LC796" class="line" lang="shell"></span>
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797
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<pre style="margin: 0;">+<span id="LC797" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#/**</span></span>
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<pre style="margin: 0;">+<span id="LC798" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </s:shelldoc></span></span>
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799
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<pre style="margin: 0;">+<span id="LC799" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#*/</span></span></pre>
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<li id="fa4f48178d1a329d4f6de31408787bc1c9c0ab80">
<a href="https://salsa.debian.org/med-team/sambamba/commit/22dc4a7940dc5de9eada1184d972cdcab89ba973#fa4f48178d1a329d4f6de31408787bc1c9c0ab80"><strong>cram/htslib.d</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">@@ -756,6 +756,7 @@ struct _Anonymous_22</td>
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756
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756
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<pre style="margin: 0;"> <span id="LC756" class="line" lang="d"> <span class="p">}</span></span>
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757
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757
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<pre style="margin: 0;"> <span id="LC757" class="line" lang="d"> <span class="n" style="color: #333;">cram_block_method</span> <span class="n" style="color: #333;">method</span><span class="p">;</span></span>
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758
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758
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<pre style="margin: 0;"> <span id="LC758" class="line" lang="d"> <span class="n" style="color: #333;">cram_block_method</span> <span class="n" style="color: #333;">orig_method</span><span class="p">;</span></span>
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759
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<pre style="margin: 0;">+<span id="LC759" class="line" lang="d"> <span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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759
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760
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<pre style="margin: 0;"> <span id="LC760" class="line" lang="d"><span class="cm" style="color: #998; font-style: italic;"> enum cram_content_type</span></span>
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760
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761
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<pre style="margin: 0;"> <span id="LC761" class="line" lang="d"><span class="cm" style="color: #998; font-style: italic;"> {</span></span>
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761
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762
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<pre style="margin: 0;"> <span id="LC762" class="line" lang="d"><span class="cm" style="color: #998; font-style: italic;"> CT_ERROR = -1,</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="767" 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">@@ -766,6 +767,7 @@ struct _Anonymous_22</td>
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766
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767
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<pre style="margin: 0;"> <span id="LC767" class="line" lang="d"><span class="cm" style="color: #998; font-style: italic;"> EXTERNAL = 4,</span></span>
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767
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768
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<pre style="margin: 0;"> <span id="LC768" class="line" lang="d"><span class="cm" style="color: #998; font-style: italic;"> CORE = 5</span></span>
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768
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769
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<pre style="margin: 0;"> <span id="LC769" class="line" lang="d"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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770
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<pre style="margin: 0;">+<span id="LC770" class="line" lang="d"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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769
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771
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<pre style="margin: 0;"> <span id="LC771" class="line" lang="d"> <span class="n" style="color: #333;">cram_content_type</span> <span class="n" style="color: #333;">content_type</span><span class="p">;</span></span>
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770
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772
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<pre style="margin: 0;"> <span id="LC772" class="line" lang="d"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">content_id</span><span class="p">;</span></span>
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771
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773
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<pre style="margin: 0;"> <span id="LC773" class="line" lang="d"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">comp_size</span><span class="p">;</span></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">@@ -833,6 +835,7 @@ struct cram_map</td>
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833
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835
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<pre style="margin: 0;"> <span id="LC835" class="line" lang="d"></span>
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834
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836
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<pre style="margin: 0;"> <span id="LC836" class="line" lang="d"><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">_Anonymous_24</span></span>
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837
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<pre style="margin: 0;"> <span id="LC837" class="line" lang="d"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC838" class="line" lang="d"> <span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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836
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839
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<pre style="margin: 0;"> <span id="LC839" class="line" lang="d"><span class="cm" style="color: #998; font-style: italic;"> enum cram_content_type</span></span>
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837
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840
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<pre style="margin: 0;"> <span id="LC840" class="line" lang="d"><span class="cm" style="color: #998; font-style: italic;"> {</span></span>
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838
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841
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<pre style="margin: 0;"> <span id="LC841" class="line" lang="d"><span class="cm" style="color: #998; font-style: italic;"> CT_ERROR = -1,</span></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">@@ -843,6 +846,7 @@ struct _Anonymous_24</td>
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843
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846
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<pre style="margin: 0;"> <span id="LC846" class="line" lang="d"><span class="cm" style="color: #998; font-style: italic;"> EXTERNAL = 4,</span></span>
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844
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847
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<pre style="margin: 0;"> <span id="LC847" class="line" lang="d"><span class="cm" style="color: #998; font-style: italic;"> CORE = 5</span></span>
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845
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848
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<pre style="margin: 0;"> <span id="LC848" class="line" lang="d"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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849
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<pre style="margin: 0;">+<span id="LC849" class="line" lang="d"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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846
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850
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<pre style="margin: 0;"> <span id="LC850" class="line" lang="d"> <span class="n" style="color: #333;">cram_content_type</span> <span class="n" style="color: #333;">content_type</span><span class="p">;</span></span>
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847
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851
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<pre style="margin: 0;"> <span id="LC851" class="line" lang="d"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ref_seq_id</span><span class="p">;</span></span>
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848
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852
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<pre style="margin: 0;"> <span id="LC852" class="line" lang="d"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ref_seq_start</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">#!/usr/bin/env python<span class="idiff left right">2</span></span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">#!/usr/bin/env python</span></span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">__future__</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">print_function</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">re</span><span class="p">,</span> <span class="n" style="color: #333;">sys</span><span class="p">,</span> <span class="n" style="color: #333;">subprocess</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -10,7 +10,7 @@ if len(sys.argv) < 2:</td>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"><span class="n" style="color: #333;">ldc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">"ldmd2"</span><span class="p">,</span> <span class="s" style="color: #d14;">"ldc2"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"><span class="n" style="color: #333;">ldc_output</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Popen</span><span class="p">([</span><span class="n" style="color: #333;">ldc</span><span class="p">,</span> <span class="s" style="color: #d14;">'-version'</span><span class="p">],</span> <span class="n" style="color: #333;">stdout</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PIPE</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">communicate</span><span class="p">()[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"><span class="n" style="color: #333;">version_re</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">r"""^.+\((?P<LDC>[^\)]+)\):\n\s*based on DMD (?P<DMD>\S+) and LLVM (?P<LLVM>\S+)\n(?:\s*built with (?P<BOOTSTRAP>.*)\n)?"""</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="python"><span class="n" style="color: #333;">match</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">match</span><span class="p">(</span><span class="n" style="color: #333;">version_re</span><span class="p">,</span> <span class="n" style="color: #333;">ldc_output</span><span class="p">,</span> <span class="n" style="color: #333;">re</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">MULTILINE</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"><span class="n" style="color: #333;">match</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">match</span><span class="p">(</span><span class="n" style="color: #333;">version_re</span><span class="p">,</span> <span class="n" style="color: #333;">ldc_output</span><span class="o" style="font-weight: 600;"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">decode</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"utf-8"</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">,</span> <span class="n" style="color: #333;">re</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">MULTILINE</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">match</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="s" style="color: #d14;">"ERROR: failed to generated LDC version information"</span><span class="p">)</span></span>
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<li id="da8c3529949805abe1b73685532823c3fb63b1a9">
<a href="https://salsa.debian.org/med-team/sambamba/commit/22dc4a7940dc5de9eada1184d972cdcab89ba973#da8c3529949805abe1b73685532823c3fb63b1a9"><strong>run_tests.sh</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/<span class="idiff left right">usr/bin/env ba</span>sh</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/<span class="idiff left right">bin/</span>sh</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># download shunit2 in order to run tests:</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># curl -L "https://dl.dropboxusercontent.com/u/7916095/shunit2-2.0.3.tgz" | tar zx --overwrite</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="shell">./test/test_suite.sh | <span class="nb" style="color: #0086b3;">tee</span> /dev/stderr | <span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: navy;">-q</span> <span class="s1" style="color: #d14;">'success rate: 100%'</span></span></pre>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Running tests..."</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell">./test/test_suite.sh 2>&1 | <span class="nb" style="color: #0086b3;">tr</span> <span class="s1" style="color: #d14;">'\r'</span> <span class="s1" style="color: #d14;">'\n'</span> <span class="o" style="font-weight: 600;">></span> test.log</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat </span>test.log</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat </span>test.log | <span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: navy;">-q</span> <span class="s1" style="color: #d14;">'success rate: 100%'</span></span></pre>
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<li id="3b3ae0b610f6ae26ed107e183c7ee027e957b1ed">
<a href="https://salsa.debian.org/med-team/sambamba/commit/22dc4a7940dc5de9eada1184d972cdcab89ba973#3b3ae0b610f6ae26ed107e183c7ee027e957b1ed"><strong>sambamba/main.d</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">@@ -19,7 +19,9 @@</td>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="d"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="d"><span class="cm" style="color: #998; font-style: italic;">*/</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="d"></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="d"><span class="k" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">std</span><span class="p">.</span><span class="n" style="color: #333;">algorithm</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="d"><span class="k" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">std</span><span class="p">.</span><span class="n" style="color: #333;">experimental</span><span class="p">.</span><span class="n" style="color: #333;">logger</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="d"><span class="k" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">std</span><span class="p">.</span><span class="n" style="color: #333;">range</span><span class="p">.</span><span class="n" style="color: #333;">primitives</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="d"></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="d"><span class="k" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">sambamba</span><span class="p">.</span><span class="n" style="color: #333;">depth</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="d"><span class="k" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">sambamba</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">;</span></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">@@ -73,6 +75,10 @@ Usage: sambamba [command] [args...]</td>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="d"></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="d"><span class="s" style="color: #d14;">To get help on a particular command, call it without args.</span></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="d"></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="d"><span class="s" style="color: #d14;">Global options</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="d"></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="d"><span class="s" style="color: #d14;"> -q quiet mode (do not show banner)</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="d"></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="d"><span class="s" style="color: #d14;">For bug reports and feature requests see</span></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="d"></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="d"><span class="s" style="color: #d14;"> https://github.com/biod/</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="87" 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">@@ -81,7 +87,7 @@ For bug reports and feature requests see</td>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="d"></span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="d"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">printVersion</span><span class="p">()</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="d"> <span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">writeln</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="d"> <span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">writeln</span><span class="p">(</span><span class="s" style="color: #d14;">"sambamba "</span> <span class="p">~</span> <span class="n" style="color: #333;">VERSION</span> <span class="p">~</span> <span class="s" style="color: #d14;">" by Artem Tarasov and Pjotr Prins (C) 2012-201<span class="idiff left right">7</span>"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="d"> <span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">writeln</span><span class="p">(</span><span class="s" style="color: #d14;">"sambamba "</span> <span class="p">~</span> <span class="n" style="color: #333;">VERSION</span> <span class="p">~</span> <span class="s" style="color: #d14;">" by Artem Tarasov and Pjotr Prins (C) 2012-201<span class="idiff left right">8</span>"</span><span class="p">);</span></span>
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91
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="d"> <span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">writeln</span><span class="p">(</span><span class="s" style="color: #d14;">" LDC "</span> <span class="p">~</span> <span class="n" style="color: #333;">LDC_VERSION_STRING</span> <span class="p">~</span> <span class="s" style="color: #d14;">" / DMD "</span> <span class="p">~</span> <span class="n" style="color: #333;">DMD_VERSION_STRING</span> <span class="p">~</span></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="d"> <span class="s" style="color: #d14;">" / LLVM"</span> <span class="p">~</span> <span class="n" style="color: #333;">LLVM_VERSION_STRING</span> <span class="p">~</span> <span class="s" style="color: #d14;">" / bootstrap "</span> <span class="p">~</span> <span class="n" style="color: #333;">BOOTSTRAP_VERSION_STRING</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="d"> <span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">writeln</span><span class="p">();</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="95" 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">@@ -89,14 +95,16 @@ void printVersion() {</td>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="d"></span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="d"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">main</span><span class="p">(</span><span class="nb" style="color: #0086b3;">string</span><span class="p">[]</span> <span class="n" style="color: #333;">args</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="d"> <span class="n" style="color: #333;">globalLogLevel</span><span class="p">(</span><span class="n" style="color: #333;">LogLevel</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="d"> <span class="n" style="color: #333;">printVersion</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="d"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="s" style="color: #d14;">"-q"</span><span class="p">).</span><span class="n" style="color: #333;">empty</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="d"> <span class="n" style="color: #333;">printVersion</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="d"></span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="d"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">length</span> <span class="p">==</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="d"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">args2</span> <span class="p">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">!(</span><span class="n" style="color: #333;">a</span> <span class="p">=></span> <span class="n" style="color: #333;">a</span> <span class="p">==</span> <span class="s" style="color: #d14;">"-q"</span><span class="p">);</span></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="d"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">args2</span><span class="p">.</span><span class="n" style="color: #333;">length</span> <span class="p">==</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="d"> <span class="n" style="color: #333;">printUsage</span><span class="p">();</span></span>
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96
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104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="d"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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97
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105
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="d"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="d"></span>
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="d"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">_args</span> <span class="p">=</span> <span class="n" style="color: #333;">args</span><span class="p"><span class="idiff left">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="p"><span class="idiff">~</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">args</span></span><span class="p">[</span><span class="mi" style="color: #099;">2</span> <span class="p">..</span> <span class="p">$];</span></span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="d"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">_args</span> <span class="p">=</span> <span class="n" style="color: #333;">args<span class="idiff left">2</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="p"><span class="idiff">~</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">args2</span></span><span class="p">[</span><span class="mi" style="color: #099;">2</span> <span class="p">..</span> <span class="p">$];</span></span>
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108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="d"></span>
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="d"> <span class="k" style="font-weight: 600;">switch</span> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span> <span class="p">{</span></span>
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102
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110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="d"> <span class="k" style="font-weight: 600;">case</span> <span class="s" style="color: #d14;">"view"</span><span class="p">:</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">view_main</span><span class="p">(</span><span class="n" style="color: #333;">_args</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/sambamba/commit/22dc4a7940dc5de9eada1184d972cdcab89ba973#b888d326ed4b8a8c518a69a5de5f0ae9bc642ef9"><strong>sambamba/markdup.d</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="37" 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">@@ -37,6 +37,9 @@ import std.traits, std.typecons, std.range, std.algorithm, std.parallelism,</td>
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37
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="d"> <span class="n" style="color: #333;">std</span><span class="p">.</span><span class="n" style="color: #333;">exception</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="p">.</span><span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="p">.</span><span class="n" style="color: #333;">typetuple</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="p">.</span><span class="n" style="color: #333;">conv</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="p">.</span><span class="n" style="color: #333;">bitmanip</span><span class="p">,</span></span>
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38
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="d"> <span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">stdc</span><span class="p">.</span><span class="n" style="color: #333;">stdlib</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="p">.</span><span class="n" style="color: #333;">datetime</span><span class="p">,</span> <span class="n" style="color: #333;">undead</span><span class="p">.</span><span class="n" style="color: #333;">stream</span> <span class="p">:</span> <span class="n" style="color: #333;">BufferedFile</span><span class="p">,</span> <span class="n" style="color: #333;">FileMode</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="d"></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="d"><span class="k" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">std</span><span class="p">.</span><span class="n" style="color: #333;">datetime</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="d"><span class="k" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">std</span><span class="p">.</span><span class="n" style="color: #333;">datetime</span><span class="p">.</span><span class="n" style="color: #333;">stopwatch</span> <span class="p">:</span> <span class="n" style="color: #333;">benchmark</span><span class="p">,</span> <span class="n" style="color: #333;">StopWatch</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="d"></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="d"><span class="c1" style="color: #998; font-style: italic;">/// Read + its index (0-based)</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="d"><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">IndexedBamRead</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="d"> <span class="kt" style="color: #458; font-weight: 600;">ulong</span> <span class="n" style="color: #333;">index</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="270" 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="273" 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">@@ -270,7 +273,7 @@ struct CollateReadPairRange(R, bool keepFragments, alias charsHashFunc)</td>
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270
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273
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<pre style="margin: 0;"> <span id="LC273" class="line" lang="d"> <span class="k" style="font-weight: 600;">version</span><span class="p">(</span><span class="n" style="color: #333;">profile</span><span class="p">)</span> <span class="p">{</span></span>
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271
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274
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<pre style="margin: 0;"> <span id="LC274" class="line" lang="d"> <span class="p">~</span><span class="k" style="font-weight: 600;">this</span><span class="p">()</span> <span class="p">{</span></span>
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272
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<pre style="margin: 0;"> <span id="LC275" class="line" lang="d"> <span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">writeln</span><span class="p">(</span><span class="s" style="color: #d14;">"duped during compaction: "</span><span class="p">,</span> <span class="n" style="color: #333;">_duped_during_compaction</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC273" class="line" lang="d"> <span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">writeln</span><span class="p">(</span><span class="s" style="color: #d14;">"time spent on compaction: "</span><span class="p">,</span> <span class="n" style="color: #333;">_compact_sw</span><span class="p">.</span><span class="n" style="color: #333;">peek</span><span class="p">().</span><span class="n" style="color: #333;"><span class="idiff left right">msecs</span></span><span class="p">,</span> <span class="s" style="color: #d14;">" ms"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="d"> <span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">writeln</span><span class="p">(</span><span class="s" style="color: #d14;">"time spent on compaction: "</span><span class="p">,</span> <span class="n" style="color: #333;">_compact_sw</span><span class="p">.</span><span class="n" style="color: #333;">peek</span><span class="p">().</span><span class="n" style="color: #333;"><span class="idiff left">total</span></span><span class="p"><span class="idiff">!</span></span><span class="s" style="color: #d14;"><span class="idiff right">"msecs"</span></span><span class="p">,</span> <span class="s" style="color: #d14;">" ms"</span><span class="p">);</span></span>
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277
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="d"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC278" class="line" lang="d"> <span class="p">}</span></span>
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279
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<pre style="margin: 0;"> <span id="LC279" class="line" lang="d"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="715" 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>
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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">@@ -715,12 +718,12 @@ auto collectSingleEndInfo(IndexedBamRead read, ReadGroupIndex read_group_index)</td>
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715
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718
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<pre style="margin: 0;"> <span id="LC718" class="line" lang="d"> <span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">coord</span> <span class="p">=</span> <span class="n" style="color: #333;">computeFivePrimeCoord</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">);</span></span>
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716
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719
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<pre style="margin: 0;"> <span id="LC719" class="line" lang="d"> <span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">idx</span> <span class="p">=</span> <span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">;</span></span>
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717
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720
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<pre style="margin: 0;"> <span id="LC720" class="line" lang="d"> <span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">score</span> <span class="p">=</span> <span class="n" style="color: #333;">computeScore</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">);</span></span>
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718
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<pre style="margin: 0;">-<span id="LC718" class="line" lang="d"> <span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">ref_id</span> <span class="p">=</span> <span class="k" style="font-weight: 600;"><span class="idiff left">cast</span></span><span class="p"><span class="idiff">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">ushort</span></span><span class="p"><span class="idiff right">)</span></span><span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">ref_id</span><span class="p">;</span></span>
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721
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<pre style="margin: 0;">+<span id="LC721" class="line" lang="d"> <span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">ref_id</span> <span class="p">=</span> <span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">ref_id</span><span class="p">;</span></span>
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719
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722
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<pre style="margin: 0;"> <span id="LC722" class="line" lang="d"> <span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">reversed</span> <span class="p">=</span> <span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">is_reverse_strand</span> <span class="p">?</span> <span class="mi" style="color: #099;">1</span> <span class="p">:</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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720
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723
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<pre style="margin: 0;"> <span id="LC723" class="line" lang="d"> <span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">paired</span> <span class="p">=</span> <span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">is_paired</span> <span class="p">&&</span> <span class="p">!</span><span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">mate_is_unmapped</span><span class="p">)</span> <span class="p">?</span> <span class="mi" style="color: #099;">1</span> <span class="p">:</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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721
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724
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<pre style="margin: 0;"> <span id="LC724" class="line" lang="d"></span>
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722
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725
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<pre style="margin: 0;"> <span id="LC725" class="line" lang="d"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">rg</span> <span class="p">=</span> <span class="n" style="color: #333;">read_group_index</span><span class="p">.</span><span class="n" style="color: #333;">getId</span><span class="p">(</span><span class="n" style="color: #333;">getRG</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">));</span></span>
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<pre style="margin: 0;">-<span id="LC723" class="line" lang="d"> <span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">library_id</span> <span class="p">=</span> <span class="k" style="font-weight: 600;"><span class="idiff left">cast</span></span><span class="p"><span class="idiff">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">short</span></span><span class="p"><span class="idiff right">)</span></span><span class="n" style="color: #333;">read_group_index</span><span class="p">.</span><span class="n" style="color: #333;">getLibraryId</span><span class="p">(</span><span class="n" style="color: #333;">rg</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC726" class="line" lang="d"> <span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">library_id</span> <span class="p">=</span> <span class="n" style="color: #333;">read_group_index</span><span class="p">.</span><span class="n" style="color: #333;">getLibraryId</span><span class="p">(</span><span class="n" style="color: #333;">rg</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC727" class="line" lang="d"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">result</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC728" class="line" lang="d"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC729" class="line" lang="d"></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">@@ -1071,7 +1074,9 @@ auto getDuplicateOffsets(R)(R reads, ReadGroupIndex rg_index,</td>
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1071
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<td class="diff-line-num new_line" data-linenumber="1074" 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">
1074
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<pre style="margin: 0;"> <span id="LC1074" class="line" lang="d"> <span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">" collecting indices of duplicate reads... "</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1072" 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">
1072
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<td class="diff-line-num new_line" data-linenumber="1075" 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">
1075
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<pre style="margin: 0;"> <span id="LC1075" class="line" lang="d"> <span class="n" style="color: #333;">sw</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">();</span></span>
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<td class="diff-line-num old_line" data-linenumber="1073" 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">
1073
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<td class="diff-line-num new_line" data-linenumber="1076" 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">
1076
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<pre style="margin: 0;"> <span id="LC1076" class="line" lang="d"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">duplicates</span> <span class="p">=</span> <span class="n" style="color: #333;">collectDuplicates</span><span class="p">(</span><span class="n" style="color: #333;">paired_ends</span><span class="p">,</span> <span class="n" style="color: #333;">single_ends</span><span class="p">,</span> <span class="n" style="color: #333;">second_ends</span><span class="p">,</span> <span class="n" style="color: #333;">cfg</span><span class="p">,</span> <span class="n" style="color: #333;">pool</span><span class="p">);</span></span>
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1074
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<td class="diff-line-num new_line old" data-linenumber="1077" 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="LC1074" class="line" lang="d"> <span class="n" style="color: #333;">sw</span><span class="p">.</span><span class="n" style="color: #333;">stop</span><span class="p">();</span> <span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">writeln</span><span class="p">(</span><span class="s" style="color: #d14;">" done in "</span><span class="p">,</span> <span class="n" style="color: #333;">sw</span><span class="p">.</span><span class="n" style="color: #333;">peek</span><span class="p">().</span><span class="n" style="color: #333;">msecs</span><span class="p">,</span> <span class="s" style="color: #d14;">" ms"</span><span class="p">);</span> <span class="n" style="color: #333;">sw</span><span class="p">.</span><span class="n" style="color: #333;">reset</span><span class="p">();</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1077" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1077
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<pre style="margin: 0;">+<span id="LC1077" class="line" lang="d"> <span class="n" style="color: #333;">sw</span><span class="p">.</span><span class="n" style="color: #333;">stop</span><span class="p">();</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1078" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1078
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<pre style="margin: 0;">+<span id="LC1078" class="line" lang="d"> <span class="k" style="font-weight: 600;">immutable</span> <span class="n" style="color: #333;">t</span> <span class="p">=</span> <span class="n" style="color: #333;">sw</span><span class="p">.</span><span class="n" style="color: #333;">peek</span><span class="p">();</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1079" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1079
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<pre style="margin: 0;">+<span id="LC1079" class="line" lang="d"> <span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">writeln</span><span class="p">(</span><span class="s" style="color: #d14;">" done in "</span><span class="p">,</span> <span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">total</span><span class="p">!</span><span class="s" style="color: #d14;">"msecs"</span><span class="p">,</span> <span class="s" style="color: #d14;">" ms"</span><span class="p">);</span> <span class="n" style="color: #333;">sw</span><span class="p">.</span><span class="n" style="color: #333;">reset</span><span class="p">();</span></span>
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1075
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<td class="diff-line-num new_line" data-linenumber="1080" 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">
1080
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<pre style="margin: 0;"> <span id="LC1080" class="line" lang="d"> <span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">writeln</span><span class="p">(</span><span class="s" style="color: #d14;">" found "</span><span class="p">,</span> <span class="n" style="color: #333;">duplicates</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">,</span> <span class="s" style="color: #d14;">" duplicates"</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1076" 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">
1076
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<td class="diff-line-num new_line" data-linenumber="1081" 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">
1081
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<pre style="margin: 0;"> <span id="LC1081" class="line" lang="d"></span>
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<td class="diff-line-num old_line" data-linenumber="1077" 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">
1077
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<td class="diff-line-num new_line" data-linenumber="1082" 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">
1082
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<pre style="margin: 0;"> <span id="LC1082" class="line" lang="d"> <span class="n" style="color: #333;">paired_ends</span><span class="p">.</span><span class="n" style="color: #333;">removeTemporaryFiles</span><span class="p">();</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1256" 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="1261" 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">@@ -1256,9 +1261,7 @@ int markdup_main(string[] args) {</td>
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1256
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<td class="diff-line-num new_line" data-linenumber="1261" 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">
1261
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<pre style="margin: 0;"> <span id="LC1261" class="line" lang="d"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">dup_idx_storage</span> <span class="p">=</span> <span class="n" style="color: #333;">getDuplicateOffsets</span><span class="p">(</span><span class="n" style="color: #333;">reads</span><span class="p">,</span> <span class="n" style="color: #333;">rg_index</span><span class="p">,</span> <span class="n" style="color: #333;">taskPool</span><span class="p">,</span> <span class="n" style="color: #333;">cfg</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1257" 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">
1257
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<td class="diff-line-num new_line" data-linenumber="1262" 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">
1262
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<pre style="margin: 0;"> <span id="LC1262" class="line" lang="d"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1258" 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">
1258
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<td class="diff-line-num new_line" data-linenumber="1263" 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">
1263
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<pre style="margin: 0;"> <span id="LC1263" class="line" lang="d"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">elapsed</span> <span class="p">=</span> <span class="n" style="color: #333;">sw</span><span class="p">.</span><span class="n" style="color: #333;">peek</span><span class="p">();</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1259" 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">
1259
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<td class="diff-line-num new_line old" data-linenumber="1264" 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="LC1259" class="line" lang="d"> <span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">writeln</span><span class="p">(</span><span class="s" style="color: #d14;">"collected list of positions in "</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1260" 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">
1260
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<td class="diff-line-num new_line old" data-linenumber="1264" 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="LC1260" class="line" lang="d"> <span class="n" style="color: #333;">elapsed</span><span class="p">.</span><span class="n" style="color: #333;">seconds</span> <span class="p">/</span> <span class="mi" style="color: #099;">60</span><span class="p">,</span> <span class="s" style="color: #d14;">" min "</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1261" 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">
1261
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<td class="diff-line-num new_line old" data-linenumber="1264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1261" class="line" lang="d"> <span class="n" style="color: #333;">elapsed</span><span class="p">.</span><span class="n" style="color: #333;">seconds</span> <span class="p">%</span> <span class="mi" style="color: #099;">60</span><span class="p">,</span> <span class="s" style="color: #d14;">" sec"</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1262" style="width: 35px; color: rgba(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="1264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1264
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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="LC1264" class="line" lang="d"> <span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">writeln</span><span class="p">(</span><span class="s" style="color: #d14;">"collected list of positions in "</span><span class="p">,</span><span class="n" style="color: #333;">elapsed</span><span class="p">.</span><span class="n" style="color: #333;">total</span><span class="p">!</span><span class="s" style="color: #d14;">"minutes"</span><span class="p">,</span><span class="s" style="color: #d14;">" min "</span><span class="p">,</span><span class="n" style="color: #333;">elapsed</span><span class="p">.</span><span class="n" style="color: #333;">total</span><span class="p">!</span><span class="s" style="color: #d14;">"seconds"</span> <span class="p">%</span> <span class="mi" style="color: #099;">60</span><span class="p">,</span><span class="s" style="color: #d14;">" sec"</span><span class="p">);</span></span>
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1262
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<td class="diff-line-num new_line" data-linenumber="1265" 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">
1265
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<pre style="margin: 0;"> <span id="LC1265" class="line" lang="d"></span>
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<pre style="margin: 0;"> <span id="LC1266" class="line" lang="d"> <span class="c1" style="color: #998; font-style: italic;">// marking or removing duplicates</span></span>
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1267
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<pre style="margin: 0;"> <span id="LC1267" class="line" lang="d"> <span class="n" style="color: #333;">bam</span> <span class="p">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">MultiBamReader</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">[</span><span class="mi" style="color: #099;">1</span> <span class="p">..</span> <span class="p">$-</span><span class="mi" style="color: #099;">1</span><span class="p">]);</span> <span class="c1" style="color: #998; font-style: italic;">// FIXME: initialized twice</span></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">@@ -1298,9 +1301,8 @@ int markdup_main(string[] args) {</td>
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1301
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<pre style="margin: 0;"> <span id="LC1301" class="line" lang="d"> <span class="p">}</span></span>
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1302
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<pre style="margin: 0;"> <span id="LC1302" class="line" lang="d"></span>
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1300
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1303
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<pre style="margin: 0;"> <span id="LC1303" class="line" lang="d"> <span class="n" style="color: #333;">sw</span><span class="p">.</span><span class="n" style="color: #333;">stop</span><span class="p">();</span></span>
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1301
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<pre style="margin: 0;">-<span id="LC1301" class="line" lang="d"> <span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">writeln</span><span class="p">(</span><span class="s" style="color: #d14;">"total time elapsed: "</span><span class="p">,</span></span>
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1302
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<pre style="margin: 0;">-<span id="LC1302" class="line" lang="d"> <span class="n" style="color: #333;">sw</span><span class="p">.</span><span class="n" style="color: #333;">peek</span><span class="p">().</span><span class="n" style="color: #333;">seconds</span> <span class="p">/</span> <span class="mi" style="color: #099;">60</span><span class="p">,</span> <span class="s" style="color: #d14;">" min "</span><span class="p">,</span></span>
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1303
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<td class="diff-line-num new_line old" data-linenumber="1304" 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="LC1303" class="line" lang="d"> <span class="n" style="color: #333;">sw</span><span class="p">.</span><span class="n" style="color: #333;">peek</span><span class="p">().</span><span class="n" style="color: #333;">seconds</span> <span class="p">%</span> <span class="mi" style="color: #099;">60</span><span class="p">,</span> <span class="s" style="color: #d14;">" sec"</span><span class="p">);</span></span>
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1304
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<pre style="margin: 0;">+<span id="LC1304" class="line" lang="d"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">elapsed2</span> <span class="p">=</span> <span class="n" style="color: #333;">sw</span><span class="p">.</span><span class="n" style="color: #333;">peek</span><span class="p">();</span></span>
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1305
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<pre style="margin: 0;">+<span id="LC1305" class="line" lang="d"> <span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">writeln</span><span class="p">(</span><span class="s" style="color: #d14;">"collected list of positions in "</span><span class="p">,</span><span class="n" style="color: #333;">elapsed2</span><span class="p">.</span><span class="n" style="color: #333;">total</span><span class="p">!</span><span class="s" style="color: #d14;">"minutes"</span><span class="p">,</span><span class="s" style="color: #d14;">" min "</span><span class="p">,</span><span class="n" style="color: #333;">elapsed2</span><span class="p">.</span><span class="n" style="color: #333;">total</span><span class="p">!</span><span class="s" style="color: #d14;">"seconds"</span> <span class="p">%</span> <span class="mi" style="color: #099;">60</span><span class="p">,</span><span class="s" style="color: #d14;">" sec"</span><span class="p">);</span></span>
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1304
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1306
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<pre style="margin: 0;"> <span id="LC1306" class="line" lang="d"></span>
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1305
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1307
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<pre style="margin: 0;"> <span id="LC1307" class="line" lang="d"> <span class="p">}</span> <span class="k" style="font-weight: 600;">catch</span> <span class="p">(</span><span class="n" style="color: #333;">Throwable</span> <span class="n" style="color: #333;">e</span><span class="p">)</span> <span class="p">{</span></span>
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1306
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1308
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<pre style="margin: 0;"> <span id="LC1308" class="line" lang="d"> <span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">writeln</span><span class="p">(</span><span class="s" style="color: #d14;">"sambamba-markdup: "</span><span class="p">,</span> <span class="n" style="color: #333;">e</span><span class="p">.</span><span class="n" style="color: #333;">msg</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/sambamba/commit/22dc4a7940dc5de9eada1184d972cdcab89ba973#a2dfc645061c612393c9e78b784b01f62f7a0e42"><strong>test/benchmark/stats.org</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">* Performance metrics</span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">** View</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">*** 4x Intel(R) Core(TM) i5-2520M CPU @ 2.50GHz (hyperthreaded)</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">**** sambamba 0.6.8-pre3</span>
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4
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">*** 8x Intel(R) Core(TM) i7-6770HQ CPU @ 2.60GHz, 16Gb, SSD</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">#+BEGIN_SRC</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="6" style="width: 35px; color: rgba(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="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">monza:~/tmp$ time ./sambamba view /gnu/data/HG00100.chrom20.ILLUMINA.bwa.GBR.low_coverage.20130415.bam.orig > /dev/null</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="6" style="width: 35px; color: rgba(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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">sambamba 0.6.8-pre3 by Artem Tarasov and Pjotr Prins (C) 2012-2018</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="6" style="width: 35px; color: rgba(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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> LDC 1.11.0 / DMD v2.081.2 / LLVM6.0.1 / bootstrap LDC - the LLVM D compiler (0.17.6)</span>
</pre>
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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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="6" style="width: 35px; color: rgba(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">real 0m6.930s</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="6" style="width: 35px; color: rgba(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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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">user 0m26.940s</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">sys 0m0.516s</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="6" style="width: 35px; color: rgba(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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">sambamba 0.6.8-pre2 by Artem Tarasov and Pjotr Prins (C) 2012-2018</span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="6" style="width: 35px; color: rgba(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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> LDC 1.10.0 / DMD v2.080.1 / LLVM6.0.1 / bootstrap LDC - the LLVM D compiler (0.17.4)</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
20
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">real 0m6.854s</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="6" style="width: 35px; color: rgba(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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21
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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="LC21" class="line" lang="plaintext">user 0m26.456s</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="6" style="width: 35px; color: rgba(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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22
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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="LC22" class="line" lang="plaintext">sys 0m0.584s</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
24
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> linux-vdso.so.1 (0x00007ffd227fc000)</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="6" style="width: 35px; color: rgba(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"> librt.so.1 => /gnu/store/n6nvxlk2j8ysffjh3jphn1k5silnakh6-glibc-2.25/lib/librt.so.1 (0x00007f5d31082000)</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="6" style="width: 35px; color: rgba(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"> libpthread.so.0 => /gnu/store/n6nvxlk2j8ysffjh3jphn1k5silnakh6-glibc-2.25/lib/libpthread.so.0 (0x00007f5d30e64000)</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="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"> libm.so.6 => /gnu/store/n6nvxlk2j8ysffjh3jphn1k5silnakh6-glibc-2.25/lib/libm.so.6 (0x00007f5d30b52000)</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="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"> libdl.so.2 => /gnu/store/n6nvxlk2j8ysffjh3jphn1k5silnakh6-glibc-2.25/lib/libdl.so.2 (0x00007f5d3094e000)</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="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"> libgcc_s.so.1 => /gnu/store/h3z6nshhdlc8zgh4mi13x1br03xipi9r-gcc-7.2.0-lib/lib/libgcc_s.so.1 (0x00007f5d30737000)</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="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"> libc.so.6 => /gnu/store/n6nvxlk2j8ysffjh3jphn1k5silnakh6-glibc-2.25/lib/libc.so.6 (0x00007f5d30398000)</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="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"> /gnu/store/n6nvxlk2j8ysffjh3jphn1k5silnakh6-glibc-2.25/lib/ld-linux-x86-64.so.2 (0x00007f5d3128a000)</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">#+END_SRC</span>
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6
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33
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">***<span class="idiff left right">* sambamba 0.6.7</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">***<span class="idiff left right"> 8x Intel(R) Core(TM) i7-6770HQ CPU @ 2.60GHz, 16Gb, SSD (hyperthreaded)</span></span>
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8
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35
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext"></span>
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9
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36
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext">#+BEGIN_SRC sh</span>
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10
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37
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext">time ./build/sambamba view /gnu/data/HG00100.chrom20.ILLUMINA.bwa.GBR.low_coverage.20130415.bam.orig > /dev/null</span>
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11
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38
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext">#+END_SRC</span>
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12
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39
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext"></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">**** sambamba 0.6.8</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">#+BEGIN_SRC</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">sambamba 0.6.8 by Artem Tarasov and Pjotr Prins (C) 2012-2018</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"> LDC 1.10.0 / DMD v2.080.1 / LLVM6.0.1 / bootstrap LDC - the LLVM D compiler (0.17.4)</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">real 0m2.869s</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">user 0m21.972s</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">sys 0m0.356s</span>
</pre>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">#+END_SRC</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"></span>
</pre>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">**** sambamba 0.6.7</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"></span>
</pre>
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13
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54
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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="LC54" class="line" lang="plaintext">#+BEGIN_SRC</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
14
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55
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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="LC55" class="line" lang="plaintext">This version was built with:</span>
</pre>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="plaintext"> LDC 1.1.1</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -33,38 +74,80 @@ sys 0m0.344s</td>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="plaintext">#+END_SRC</span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="plaintext">** Sort</span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="plaintext">*** 56x Intel(R) Xeon(R) CPU E5-2683 v3 @ 2.00GHz, 256Gb</span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="plaintext"></span>
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39
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="plaintext">**** sambamba 0.6.6</span>
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40
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext"></span>
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41
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79
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="plaintext">#+BEGIN_SRC sh</span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="plaintext">time ./sambamba_v0.6.6 sort -m 20615843020 -N -o /dev/null ENCFF696RLQ.bam -p</span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="plaintext">#+END_SRC</span>
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44
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext">**** sambamba 0.6.8</span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext"></span>
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45
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85
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="plaintext">#+BEGIN_SRC</span>
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46
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="plaintext">This version was built with:</span>
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47
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="plaintext"> LDC 0.17.1</span>
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48
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="plaintext"> using DMD v2.068.2</span>
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<td class="diff-line-num old old_line" data-linenumber="49" 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">
49
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="plaintext"> using LLVM 3.8.0</span>
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50
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="plaintext"> bootstrapped with version not available</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext">sambamba 0.6.8 by Artem Tarasov and Pjotr Prins (C) 2012-2018</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext"> LDC 1.10.0 / DMD v2.080.1 / LLVM6.0.1 / bootstrap LDC - the LLVM D compiler (0.17.4)</span>
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51
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="plaintext">real 10m0.932s</span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="plaintext">user 151m39.172s</span>
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<td class="diff-line-num old old_line" data-linenumber="54" 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">
54
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="plaintext">sys 3m7.596s</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="plaintext">real 7m50.558s</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="plaintext">user 89m10.808s</span>
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<td class="diff-line-num new new_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext">sys 2m57.188s</span>
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<td class="diff-line-num new old_line" data-linenumber="55" style="width: 35px; color: rgba(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="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext">#+END_SRC</span>
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<td class="diff-line-num new old_line" data-linenumber="55" style="width: 35px; color: rgba(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="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext"></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="plaintext">and with 120GB RAM</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext">#+BEGIN_SRC</span>
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<td class="diff-line-num new old_line" data-linenumber="55" style="width: 35px; color: rgba(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="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext">sambamba 0.6.8 by Artem Tarasov and Pjotr Prins (C) 2012-2018</span>
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<td class="diff-line-num new old_line" data-linenumber="55" style="width: 35px; color: rgba(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="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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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext"> LDC 1.10.0 / DMD v2.080.1 / LLVM6.0.1 / bootstrap LDC - the LLVM D compiler (0.17.4)</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext">real 3m49.953s</span>
</pre>
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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">user 81m16.956s</span>
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<td class="diff-line-num new old_line" data-linenumber="55" style="width: 35px; color: rgba(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="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">sys 1m58.332s</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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext">#+END_SRC</span>
</pre>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext">**** sambamba 0.6.8-pre1</span>
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<td class="diff-line-num new new_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
107
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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="LC107" class="line" lang="plaintext">#+BEGIN_SRC</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="55" style="width: 35px; color: rgba(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="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">Wed Feb 7 03:43:14 CST 2018</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="plaintext">sambamba 0.6.8-pre1</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="55" 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">
55
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<td class="diff-line-num new_line" data-linenumber="110" 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">
110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="56" 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">
56
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<td class="diff-line-num new_line" data-linenumber="111" 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">
111
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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="LC111" class="line" lang="plaintext">This version was built with:</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="57" 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">
57
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<td class="diff-line-num new_line old" data-linenumber="112" 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="LC57" class="line" lang="plaintext"> LDC 1.1.1</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="58" 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">
58
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="plaintext"> using DMD v2.071.2</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="59" 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">
59
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<td class="diff-line-num new_line old" data-linenumber="112" 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="LC59" class="line" lang="plaintext"> using LLVM 3.9.1</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="60" 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">
60
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<td class="diff-line-num new_line old" data-linenumber="112" 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="LC60" class="line" lang="plaintext"> bootstrapped with LDC - the LLVM D compiler (1.1.1)</span>
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<td class="diff-line-num new old_line" data-linenumber="61" style="width: 35px; color: rgba(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"> LDC 1.7.0</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="61" style="width: 35px; color: rgba(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="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"> using DMD v2.077.1</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="61" style="width: 35px; color: rgba(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="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"> using LLVM 5.0.1</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="61" style="width: 35px; color: rgba(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"> bootstrapped with LDC - the LLVM D compiler (1.7.0)</span>
</pre>
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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"></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="61" style="width: 35px; color: rgba(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="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">real 8m0.528s</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="61" style="width: 35px; color: rgba(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">user 88m44.084s</span>
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<td class="diff-line-num new old_line" data-linenumber="61" style="width: 35px; color: rgba(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="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="plaintext">sys 2m45.888s</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="61" 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">
61
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<td class="diff-line-num new_line" data-linenumber="120" 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">
120
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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="LC120" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="62" 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">
62
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<td class="diff-line-num new_line old" data-linenumber="121" 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="LC62" class="line" lang="plaintext">real 9m22.501s</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="63" 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">
63
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<td class="diff-line-num new_line old" data-linenumber="121" 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="LC63" class="line" lang="plaintext">user 98m24.748s</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="64" 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">
64
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<td class="diff-line-num new_line old" data-linenumber="121" 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="LC64" class="line" lang="plaintext">sys 2m51.996s</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="65" 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">
65
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<td class="diff-line-num new_line" data-linenumber="121" 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">
121
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="plaintext">#+END_SRC</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="66" 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">
66
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<td class="diff-line-num new_line" data-linenumber="122" 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">
122
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="67" 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">
67
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<td class="diff-line-num new_line old" data-linenumber="123" 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="LC67" class="line" lang="plaintext">Note, updating compiler shows a speed gain for 0.6.6.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext">When sambamba is given enough RAM to hold everything in memory sambamba is twice</span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext">as fast (apparently half the time goes to intermediate IO)</span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="plaintext"></span>
</pre>
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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
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="plaintext">#+BEGIN_SRC sh</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="plaintext">time ./sambamba sort -N -o /dev/null ENCFF696RLQ.bam -p -m 120G</span>
</pre>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="plaintext">#+END_SRC</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="plaintext"></span>
</pre>
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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">#+BEGIN_SRC</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="plaintext">real 3m46.856s</span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="plaintext">user 81m44.524s</span>
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<td class="diff-line-num new new_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="plaintext">sys 1m56.388s</span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext">#+END_SRC</span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="plaintext"></span>
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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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<pre style="margin: 0;">+<span id="LC136" class="line" lang="plaintext">with 64GB it is</span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="plaintext"></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="plaintext">#+BEGIN_SRC</span>
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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="plaintext">real 5m36.062s</span>
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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="plaintext">user 88m43.176s</span>
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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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<pre style="margin: 0;">+<span id="LC141" class="line" lang="plaintext">sys 3m0.536s</span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="plaintext">#+END_SRC</span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="plaintext"></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="plaintext">and with 32GB it is</span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
146
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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="LC146" class="line" lang="plaintext">#+BEGIN_SRC</span>
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<td class="diff-line-num new old_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="plaintext">real 7m22.125s</span>
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<td class="diff-line-num new new_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="plaintext">user 89m6.188s</span>
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<td class="diff-line-num new new_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="plaintext">sys 2m51.228s</span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="plaintext">#+END_SRC</span>
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68
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151
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="plaintext"></span>
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69
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152
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="plaintext">**** sambamba 0.6.7</span>
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70
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153
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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="LC153" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="143" 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="226" 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">@@ -143,48 +226,109 @@ sys 2m56.244s</td>
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143
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226
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="144" 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">
144
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227
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="plaintext">So, the release is reverted an after a version bump:</span>
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145
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228
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<pre style="margin: 0;"> <span id="LC228" class="line" lang="plaintext"></span>
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146
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="plaintext">**** sambamba 0.6.<span class="idiff left right">8</span></span>
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<td class="diff-line-num new old_line" data-linenumber="147" style="width: 35px; color: rgba(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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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="plaintext">**** sambamba 0.6.<span class="idiff left right">6</span></span>
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147
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230
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<pre style="margin: 0;"> <span id="LC230" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="148" 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">
148
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231
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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="LC231" class="line" lang="plaintext">#+BEGIN_SRC</span>
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<td class="diff-line-num old old_line" data-linenumber="149" 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">
149
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="plaintext">Wed Feb 7 03:43:14 CST 2018</span>
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<td class="diff-line-num old old_line" data-linenumber="150" 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">
150
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="plaintext">sambamba 0.6.8-pre1</span>
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<td class="diff-line-num old old_line" data-linenumber="151" 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">
151
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="152" 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">
152
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<td class="diff-line-num new_line" data-linenumber="232" 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">
232
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="plaintext">This version was built with:</span>
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<td class="diff-line-num old old_line" data-linenumber="153" 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">
153
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<td class="diff-line-num new_line old" data-linenumber="233" 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="LC153" class="line" lang="plaintext"> LDC <span class="idiff left right">1.7.0</span></span>
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<td class="diff-line-num old old_line" data-linenumber="154" 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">
154
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<td class="diff-line-num new_line old" data-linenumber="233" 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="LC154" class="line" lang="plaintext"> using DMD v2.0<span class="idiff left right">77.1</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="155" 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">
155
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="plaintext"> using LLVM <span class="idiff left right">5.0.1</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="156" 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">
156
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="plaintext"> bootstrapped with <span class="idiff left right">LDC - the LLVM D compiler (1.7.0)</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="157" style="width: 35px; color: rgba(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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233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="plaintext"> LDC <span class="idiff left right">0.17.1</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="157" style="width: 35px; color: rgba(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="234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
234
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="plaintext"> using DMD v2.0<span class="idiff left right">68.2</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="157" style="width: 35px; color: rgba(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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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="plaintext"> using LLVM <span class="idiff left right">3.8.0</span></span>
</pre>
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236
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="plaintext"> bootstrapped with <span class="idiff left right">version not available</span></span>
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157
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237
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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="LC237" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="158" 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">
158
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="plaintext">real 8m0.528s</span>
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<td class="diff-line-num old old_line" data-linenumber="159" 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">
159
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="plaintext">user 88m44.084s</span>
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<td class="diff-line-num old old_line" data-linenumber="160" 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">
160
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="plaintext">sys 2m45.888s</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="161" 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">
161
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="plaintext">#+END_SRC</span>
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<td class="diff-line-num new old_line" data-linenumber="162" style="width: 35px; color: rgba(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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238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="plaintext">real 10m0.932s</span>
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<td class="diff-line-num new old_line" data-linenumber="162" style="width: 35px; color: rgba(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="239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
239
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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="LC239" class="line" lang="plaintext">user 151m39.172s</span>
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<td class="diff-line-num new old_line" data-linenumber="162" style="width: 35px; color: rgba(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="240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
240
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="plaintext">sys 3m7.596s</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="162" 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">
162
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<td class="diff-line-num new_line" data-linenumber="241" 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">
241
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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="LC241" class="line" lang="plaintext"></span>
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163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="plaintext">When sambamba is given enough RAM to hold everything in memory sambamba is twice</span>
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164
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="plaintext">as fast (apparently half the time goes to intermediate IO)</span>
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242
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="plaintext">This version was built with:</span>
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243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="plaintext"> LDC 1.1.1</span>
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244
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="plaintext"> using DMD v2.071.2</span>
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245
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="plaintext"> using LLVM 3.9.1</span>
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246
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="plaintext"> bootstrapped with LDC - the LLVM D compiler (1.1.1)</span>
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165
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247
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<pre style="margin: 0;"> <span id="LC247" class="line" lang="plaintext"></span>
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166
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="plaintext">#+BEGIN_SRC sh</span>
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167
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="plaintext">time ./sambamba sort -N -o /dev/null ENCFF696RLQ.bam -p -m 120G</span>
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248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="plaintext">real 9m22.501s</span>
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249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="plaintext">user 98m24.748s</span>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="plaintext">sys 2m51.996s</span>
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168
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251
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<pre style="margin: 0;"> <span id="LC251" class="line" lang="plaintext">#+END_SRC</span>
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169
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252
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<pre style="margin: 0;"> <span id="LC252" class="line" lang="plaintext"></span>
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170
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="plaintext">#+BEGIN_SRC</span>
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<td class="diff-line-num old old_line" data-linenumber="171" 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">
171
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="plaintext">real 3m46.856s</span>
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<td class="diff-line-num old old_line" data-linenumber="172" 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">
172
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="plaintext">user 81m44.524s</span>
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<td class="diff-line-num old old_line" data-linenumber="173" 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">
173
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="plaintext">sys 1m56.388s</span>
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<td class="diff-line-num old old_line" data-linenumber="174" 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">
174
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="plaintext">#+END_SRC</span>
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253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="plaintext">Note, updating compiler shows a speed gain for 0.6.6.</span>
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175
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254
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<pre style="margin: 0;"> <span id="LC254" class="line" lang="plaintext"></span>
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<td class="diff-line-num old old_line" data-linenumber="176" 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">
176
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="plaintext">with 64GB it is</span>
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<td class="diff-line-num new old_line" data-linenumber="177" style="width: 35px; color: rgba(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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255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="plaintext">** Markdup</span>
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256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="plaintext">*** 8x Intel(R) Core(TM) i7-6770HQ CPU @ 2.60GHz, 16Gb, SSD (hyperthreaded)</span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="plaintext"></span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="plaintext">**** sambamba 0.6.8</span>
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<td class="diff-line-num old_line" data-linenumber="177" 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">
177
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<td class="diff-line-num new_line" data-linenumber="259" 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">
259
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<pre style="margin: 0;"> <span id="LC259" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="178" 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">
178
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<td class="diff-line-num new_line" data-linenumber="260" 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">
260
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<pre style="margin: 0;"> <span id="LC260" class="line" lang="plaintext">#+BEGIN_SRC</span>
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<td class="diff-line-num old old_line" data-linenumber="179" 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">
179
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<td class="diff-line-num new_line old" data-linenumber="261" 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="LC179" class="line" lang="plaintext">real 5m36.062s</span>
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<td class="diff-line-num old old_line" data-linenumber="180" 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">
180
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<td class="diff-line-num new_line old" data-linenumber="261" 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="LC180" class="line" lang="plaintext">user 88m43.176s</span>
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<td class="diff-line-num old old_line" data-linenumber="181" 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">
181
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<td class="diff-line-num new_line old" data-linenumber="261" 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="LC181" class="line" lang="plaintext">sys 3m0.536s</span>
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<td class="diff-line-num new old_line" data-linenumber="182" style="width: 35px; color: rgba(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="261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="plaintext">sambamba 0.6.8 by Artem Tarasov and Pjotr Prins (C) 2012-2018</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="182" style="width: 35px; color: rgba(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="262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="plaintext"> LDC 1.10.0 / DMD v2.080.1 / LLVM6.0.1 / bootstrap LDC - the LLVM D compiler (0.17.4)</span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="plaintext"></span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="plaintext">finding positions of the duplicate reads in the file...</span>
</pre>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="plaintext"> sorted 11286293 end pairs</span>
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<td class="diff-line-num new old_line" data-linenumber="182" style="width: 35px; color: rgba(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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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="plaintext"> and 156042 single ends (among them 0 unmatched pairs)</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="182" style="width: 35px; color: rgba(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="267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="plaintext"> collecting indices of duplicate reads... done in 1325 ms</span>
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<td class="diff-line-num new new_line" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="plaintext"> found 6603388 duplicates</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="182" style="width: 35px; color: rgba(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="269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="plaintext">collected list of positions in 0 min 16 sec</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="182" style="width: 35px; color: rgba(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="270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="plaintext">marking duplicates...</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="182" style="width: 35px; color: rgba(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="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="plaintext">collected list of positions in 1 min 2 sec</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="182" style="width: 35px; color: rgba(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="272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="plaintext"> Command being timed: "./bin/sambamba markdup /gnu/data/in_raw.sorted.bam /gnu/data/in_raw.sorted.bam t2.bam"</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="plaintext"> User time (seconds): 406.49</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="182" style="width: 35px; color: rgba(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="274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="plaintext"> System time (seconds): 3.86</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="182" style="width: 35px; color: rgba(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="275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
275
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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="LC275" class="line" lang="plaintext"> Percent of CPU this job got: 649%</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="182" style="width: 35px; color: rgba(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="276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="plaintext"> Elapsed (wall clock) time (h:mm:ss or m:ss): 1:03.13</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="182" style="width: 35px; color: rgba(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="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
277
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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="LC277" class="line" lang="plaintext"> Average shared text size (kbytes): 0</span>
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<td class="diff-line-num new old_line" data-linenumber="182" style="width: 35px; color: rgba(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="278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
278
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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="LC278" class="line" lang="plaintext"> Average unshared data size (kbytes): 0</span>
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<td class="diff-line-num new old_line" data-linenumber="182" style="width: 35px; color: rgba(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="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
279
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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="LC279" class="line" lang="plaintext"> Average stack size (kbytes): 0</span>
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<td class="diff-line-num new old_line" data-linenumber="182" style="width: 35px; color: rgba(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="280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
280
</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="LC280" class="line" lang="plaintext"> Average total size (kbytes): 0</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="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
281
</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="LC281" class="line" lang="plaintext"> Maximum resident set size (kbytes): 1709720</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
282
</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="LC282" class="line" lang="plaintext"> Average resident set size (kbytes): 0</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="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
283
</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="LC283" class="line" lang="plaintext"> Major (requiring I/O) page faults: 0</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="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
284
</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="LC284" class="line" lang="plaintext"> Minor (reclaiming a frame) page faults: 1140382</span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="285" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
285
</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="LC285" class="line" lang="plaintext"> Voluntary context switches: 393213</span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="286" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
286
</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="LC286" class="line" lang="plaintext"> Involuntary context switches: 8993</span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="287" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
287
</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="LC287" class="line" lang="plaintext"> Swaps: 0</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="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="288" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
288
</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="LC288" class="line" lang="plaintext"> File system inputs: 0</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
289
</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="LC289" class="line" lang="plaintext"> File system outputs: 2663824</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="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
290
</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="LC290" class="line" lang="plaintext"> Socket messages sent: 0</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
291
</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="LC291" class="line" lang="plaintext"> Socket messages received: 0</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
292
</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="LC292" class="line" lang="plaintext"> Signals delivered: 0</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
293
</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="LC293" class="line" lang="plaintext"> Page size (bytes): 4096</span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="294" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
294
</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="LC294" class="line" lang="plaintext"> Exit status: 0</span>
</pre>
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</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="182" 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">
182
</td>
<td class="diff-line-num new_line" data-linenumber="295" 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">
295
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC295" class="line" lang="plaintext">#+END_SRC</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="183" 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">
183
</td>
<td class="diff-line-num new_line" data-linenumber="296" 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">
296
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC296" class="line" lang="plaintext"></span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="184" 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">
184
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<td class="diff-line-num new_line old" data-linenumber="297" 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">
</td>
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="plaintext">and with 32GB it is</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
297
</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="LC297" class="line" lang="plaintext">Uses slightly more memory but is faster than</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
298
</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="LC298" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
299
</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="LC299" class="line" lang="plaintext">**** sambamba 0.6.7-pre1</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="185" 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">
185
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<td class="diff-line-num new_line" data-linenumber="300" 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">
300
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC300" class="line" lang="plaintext"></span>
</pre>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="186" 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">
186
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<td class="diff-line-num new_line" data-linenumber="301" 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">
301
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC301" class="line" lang="plaintext">#+BEGIN_SRC</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="187" 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">
187
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<td class="diff-line-num new_line old" data-linenumber="302" 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">
</td>
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="plaintext">real 7m22.125s</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="188" 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">
188
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<td class="diff-line-num new_line old" data-linenumber="302" 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">
</td>
<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC188" class="line" lang="plaintext">user 89m6.188s</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="189" 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">
189
</td>
<td class="diff-line-num new_line old" data-linenumber="302" 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">
</td>
<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC189" class="line" lang="plaintext">sys 2m51.228s</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="plaintext">/usr/bin/time --verbose sambamba markdup /gnu/data/in_raw.sorted.bam /gnu/data/in_raw.sorted.bam t2.bam</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="190" style="width: 35px; color: rgba(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="303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="plaintext">finding positions of the duplicate reads in the file...</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="190" style="width: 35px; color: rgba(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="304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="plaintext"> sorted 11286293 end pairs</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="190" style="width: 35px; color: rgba(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="305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="plaintext"> and 156042 single ends (among them 0 unmatched pairs)</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="plaintext"> collecting indices of duplicate reads... done in 1521 ms</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="190" style="width: 35px; color: rgba(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="307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="plaintext"> found 6603388 duplicates</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="190" style="width: 35px; color: rgba(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="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="plaintext">collected list of positions in 0 min 16 sec</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="190" style="width: 35px; color: rgba(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="309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="plaintext">marking duplicates...</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="plaintext">total time elapsed: 1 min 4 sec</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="311" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="plaintext"> Command being timed: "sambamba markdup /gnu/data/in_raw.sorted.bam /gnu/data/in_raw.sorted.bam t2.bam"</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="190" style="width: 35px; color: rgba(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="312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="plaintext"> User time (seconds): 423.78</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="190" style="width: 35px; color: rgba(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="313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="plaintext"> System time (seconds): 4.47</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="190" style="width: 35px; color: rgba(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="314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="plaintext"> Percent of CPU this job got: 666%</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="190" style="width: 35px; color: rgba(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="315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="plaintext"> Elapsed (wall clock) time (h:mm:ss or m:ss): 1:04.24</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="190" style="width: 35px; color: rgba(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="316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
316
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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="LC316" class="line" lang="plaintext"> Average shared text size (kbytes): 0</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="190" style="width: 35px; color: rgba(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="317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
317
</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="LC317" class="line" lang="plaintext"> Average unshared data size (kbytes): 0</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="190" style="width: 35px; color: rgba(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="318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
318
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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="LC318" class="line" lang="plaintext"> Average stack size (kbytes): 0</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
319
</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="LC319" class="line" lang="plaintext"> Average total size (kbytes): 0</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
320
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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="LC320" class="line" lang="plaintext"> Maximum resident set size (kbytes): 1542764</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="190" style="width: 35px; color: rgba(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="321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
321
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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="LC321" class="line" lang="plaintext"> Average resident set size (kbytes): 0</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="190" style="width: 35px; color: rgba(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="322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
322
</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="LC322" class="line" lang="plaintext"> Major (requiring I/O) page faults: 0</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="190" style="width: 35px; color: rgba(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="323" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
323
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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="LC323" class="line" lang="plaintext"> Minor (reclaiming a frame) page faults: 1839470</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="190" style="width: 35px; color: rgba(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="324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
324
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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="LC324" class="line" lang="plaintext"> Voluntary context switches: 368082</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="190" style="width: 35px; color: rgba(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="325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
325
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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="LC325" class="line" lang="plaintext"> Involuntary context switches: 8537</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="190" style="width: 35px; color: rgba(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="326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
326
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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="LC326" class="line" lang="plaintext"> Swaps: 0</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="190" style="width: 35px; color: rgba(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="327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="plaintext"> File system inputs: 0</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="190" style="width: 35px; color: rgba(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="328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="plaintext"> File system outputs: 2643840</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="190" style="width: 35px; color: rgba(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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329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="plaintext"> Socket messages sent: 0</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="190" style="width: 35px; color: rgba(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="330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="plaintext"> Socket messages received: 0</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="190" style="width: 35px; color: rgba(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="331" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="plaintext"> Signals delivered: 0</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="190" style="width: 35px; color: rgba(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="332" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="plaintext"> Page size (bytes): 4096</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="190" style="width: 35px; color: rgba(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="333" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
333
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="plaintext"> Exit status: 0</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="190" 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">
190
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334
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<pre style="margin: 0;"> <span id="LC334" class="line" lang="plaintext">#+END_SRC</span></pre>
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<li id="076a163a9686c6ad68d6256408877818d28a30e8">
<a href="https://salsa.debian.org/med-team/sambamba/commit/22dc4a7940dc5de9eada1184d972cdcab89ba973#076a163a9686c6ad68d6256408877818d28a30e8"><strong>test/issue_356.sam</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">@HD VN:1.3 SO:coordinate</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">@SQ SN:chr1 LN:1575</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">@SQ SN:chr2 LN:1584</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">@RG ID:foo LB:foo PL:ILLUMINA SM:foo PU:foo CN:foo DT:2017-12-10T00:00:00-0500 PG:foo PM:HiSeq2500_HighOutput</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">EAS56_57:6:190:289:82 69 chr1 100 0 * = 100 0 CTCAAGGTTGTTGCAAGGGGGTCTATGTGAACAAA <<<7<<<;<<<<<<<<8;;<7;4<;<;;;;;94<; MF:i:192</span>
</pre>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">EAS56_57:6:190:289:82 137 chr1 100 73 35M = 100 0 AGGGGTGCAGAGCCGAGTCACGGGGTTGCCAGCAC <<<<<<;<<<<<<<<<<;<<;<<<<;8<6;9;;2; MF:i:64 Aq:i:0 NM:i:0 UQ:i:0 H0:i:1 H1:i:0</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">EAS51_64:3:190:727:308 99 chr1 103 99 35M = 263 195 GGTGCAGAGCCGAGTCACGGGGTTGCCAGCACAGG <<<<<<<<<<<<<<<<<<<<<<<<<<<::<<<844 MF:i:18 Aq:i:73 NM:i:0 UQ:i:0 H0:i:1 H1:i:0</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">EAS112_34:7:141:80:875 99 chr1 110 99 35M = 265 190 AGCCGAGTCACGGGGTTGCCAGCACAGGGGCTTAA <<<<<<<<<<<<<<<<<<<<<<:<<8;<<8+7;-7 MF:i:18 Aq:i:69 NM:i:0 UQ:i:0 H0:i:1 H1:i:0</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">EAS219_FC30151:3:40:1128:1940 163 chr1 112 99 35M = 291 214 CCGAGTCACGGGGTTGCCAGCACAGGGGCTTAACC <<<<<<<<<<<<<<<<<<<;<<5;;<<<9;;;;7: MF:i:18 Aq:i:70 NM:i:0 UQ:i:0 H0:i:1 H1:i:0</span>
</pre>
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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">EAS51_62:5:290:319:736 69 chr1 113 0 * = 113 0 GTTCTCAAGGTTGTTGCAAGGGGGTCTATGTGAAC <<<<<<:7:<.<<<<7<<.<.<<.9*<4<:<4%74 MF:i:192</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">EAS51_62:5:290:319:736 137 chr1 113 73 35M = 113 0 CGAGTCACGGGGTTGCCAGCACAGGGGCTTAACCT ==;=======7====6=;==:;;====66=::27: MF:i:64 Aq:i:0 NM:i:0 UQ:i:0 H0:i:1 H1:i:0</span>
</pre>
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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">B7_597:2:132:493:921 69 chr1 119 0 * = 119 0 GTTCTCAAGGTTGTTGCAAGGGGGTCTATGTGAAC <<<<<<<<<<<<<<<<<<<;<<<<77;0<;;6777 MF:i:192</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">B7_597:2:132:493:921 137 chr1 119 75 35M = 119 0 ACGGGGTTGCCAGCACAGGGGCTTAACCTCTGGTG <<<<<<<<<<<<<<<<;<<<<<<<<;<<<<;;88: MF:i:64 Aq:i:0 NM:i:0 UQ:i:0 H0:i:1 H1:i:0</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">EAS114_30:7:283:799:560 163 chr1 121 66 35M = 283 197 GGGGTTGCCAGCACAGGGGCTTAACCTCTGGTGAC <<<<+<<<<8<<<+<<<<<;<<:07;8;7402447 MF:i:18 Aq:i:66 NM:i:0 UQ:i:0 H0:i:1 H1:i:0</span>
</pre>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">EAS192_3:1:225:195:543 99 chr1 123 99 35M = 299 211 GGTTGCCAGCACAGGGGCTTAACCTCTGGTGACTG <<<<<<<<<<<<<<<<<<<<<<<9<<;::388998 MF:i:18 Aq:i:72 NM:i:0 UQ:i:0 H0:i:1 H1:i:0</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">B7_589:6:114:714:317 99 chr1 126 99 35M = 311 220 TGCCAGCACAGGGGCTTAACCTCTGGTGACTGCCA <<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<5;<; MF:i:18 Aq:i:75 NM:i:0 UQ:i:0 H0:i:1 H1:i:0</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">EAS114_39:1:70:147:84 163 chr1 128 73 35M = 285 192 CCAGCACAGGGGCTTAACCTCTGGTGACTGCCAGA <<<<<<<<<<<<<<<<<<<<;<<<<<<<<<;(5<< MF:i:18 Aq:i:73 NM:i:0 UQ:i:0 H0:i:1 H1:i:0</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">EAS188_7:2:187:227:818 163 chr1 129 99 35M = 290 196 CAGCACAGGGGCTTAACCTCTGGTGACTGCCAGAG <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<3<;<< MF:i:18 Aq:i:76 NM:i:0 UQ:i:0 H0:i:1 H1:i:0</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">EAS1_97:4:77:29:126 99 chr1 131 99 35M = 315 219 GCACAGGGGCTTAACCTCTGGTGACTGCCAGAGCT <<<<<<<<<<3<<<<<<<;;;7<;<<449<-:977 MF:i:18 Aq:i:69 NM:i:0 UQ:i:0 H0:i:1 H1:i:0</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">EAS114_30:4:327:795:103 99 chr1 133 99 35M = 302 204 ACAGGGGCTTAACCTCTGGTGACTGCCAGAGCTGC <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<; MF:i:18 Aq:i:75 NM:i:0 UQ:i:0 H0:i:1 H1:i:0</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">EAS114_30:3:139:117:262 69 chr1 135 0 * = 135 0 GTTCTCAAGGTTGTTGCAAGGGGGTCTATGTGAAC <<<7<<<<<<<<<<<<<<<<<<<;<;<<<<<37;3 MF:i:192</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">EAS114_30:3:139:117:262 137 chr1 135 76 35M = 135 0 AGGGGCTTAACCTCTGGTGACTGCCAGAGCTGCTG <<<<;<<<<<<<<<<<<<:<<<<<:<<8<<<<:<: MF:i:64 Aq:i:0 NM:i:0 UQ:i:0 H0:i:1 H1:i:0</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">EAS219_FC30151:5:29:817:854 73 chr1 135 77 35M = 135 0 AGGGGCTTAACCTCTGGTGACTGCCAGAGCTGCTG <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< MF:i:64 Aq:i:0 NM:i:0 UQ:i:0 H0:i:1 H1:i:0</span></pre>
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<a href="https://salsa.debian.org/med-team/sambamba/commit/22dc4a7940dc5de9eada1184d972cdcab89ba973#3708ce0a178d356e1f2b2d1b351aeb02556a5a7a"><strong>test/test_suite.sh</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/<span class="idiff left right">usr/bin/env ba</span>sh</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/<span class="idiff left right">bin/</span>sh</span></span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="shell"></span>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="shell"><span class="nv" style="color: teal;">sambamba</span><span class="o" style="font-weight: 600;">=</span>./bin/sambamba</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: teal;">opts</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"-q"</span></span>
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4
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="shell"><span class="nv" style="color: teal;">outdir</span><span class="o" style="font-weight: 600;">=</span>output</span>
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5
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell"><span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: navy;">-p</span> <span class="nv" style="color: teal;">$outdir</span></span>
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6
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="shell"></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="nb" style="color: #0086b3;">md5sum</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span>which <span class="nb" style="color: #0086b3;">md5sum</span><span class="sb" style="color: #d14;">`</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-z</span> <span class="nv" style="color: teal;">$md5sum</span> <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">md5sum</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"md5 -r "</span> <span class="c" style="color: #998; font-style: italic;"># for OSX</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"></span>
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7
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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;"># Name sorted and pos sorted</span></span>
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8
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="shell"><span class="nv" style="color: teal;">nsortedbam</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">$outdir</span>/ex1_header.nsorted.bam</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="shell"><span class="nv" style="color: teal;">sortedbam</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">$outdir</span>/ex1_header.sorted.bam</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">@@ -11,43 +15,43 @@ sortedbam=$outdir/ex1_header.sorted.bam</td>
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11
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="shell">testSamtoBam<span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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12
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="shell"> <span class="nv" style="color: teal;">outfn</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">$nsortedbam</span></span>
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13
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># first identity SAM but without header</span></span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> view <span class="nt" style="color: navy;">-S</span> <span class="nb" style="color: #0086b3;">test</span>/ex1_header.sam <span class="nt" style="color: navy;">-f</span> sam <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: teal;">$nsortedbam</span>.sam.1</span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="shell"> assertEquals <span class="s2" style="color: #d14;">"ff5d66e6cd1cab4e8e6330f2829b7c41"</span> <span class="k" style="font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">md5sum</span> <span class="nv" style="color: teal;">$nsortedbam</span>.sam.1 |cut <span class="nt" style="color: navy;">-c</span> 1-32<span class="k" style="font-weight: 600;">)</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> <span class="nv" style="color: teal;"><span class="idiff left">$opts</span></span><span class="idiff right"> </span>view <span class="nt" style="color: navy;">-S</span> <span class="nb" style="color: #0086b3;">test</span>/ex1_header.sam <span class="nt" style="color: navy;">-f</span> sam <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: teal;">$nsortedbam</span>.sam.1</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"> assertEquals <span class="s2" style="color: #d14;">"ff5d66e6cd1cab4e8e6330f2829b7c41"</span> <span class="k" style="font-weight: 600;">$(</span><span class="nv" style="color: teal;"><span class="idiff left right">$</span>md5sum</span> <span class="nv" style="color: teal;">$nsortedbam</span>.sam.1 |cut <span class="nt" style="color: navy;">-c</span> 1-32<span class="k" style="font-weight: 600;">)</span></span>
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16
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># now convert to BAM</span></span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> view <span class="nt" style="color: navy;">-S</span> <span class="nb" style="color: #0086b3;">test</span>/ex1_header.sam <span class="nt" style="color: navy;">-f</span> bam <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: teal;">$nsortedbam</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> <span class="nv" style="color: teal;"><span class="idiff left">$opts</span></span><span class="idiff right"> </span>view <span class="nt" style="color: navy;">-S</span> <span class="nb" style="color: #0086b3;">test</span>/ex1_header.sam <span class="nt" style="color: navy;">-f</span> bam <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: teal;">$nsortedbam</span></span>
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18
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># BAM back to identity</span></span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> view <span class="nv" style="color: teal;">$nsortedbam</span> <span class="nt" style="color: navy;">-f</span> sam <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: teal;">$nsortedbam</span>.sam.2</span>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="shell"> assertEquals <span class="s2" style="color: #d14;">"ff5d66e6cd1cab4e8e6330f2829b7c41"</span> <span class="k" style="font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">md5sum</span> <span class="nv" style="color: teal;">$nsortedbam</span>.sam.2 |cut <span class="nt" style="color: navy;">-c</span> 1-32<span class="k" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> <span class="nv" style="color: teal;"><span class="idiff left">$opts</span></span><span class="idiff right"> </span>view <span class="nv" style="color: teal;">$nsortedbam</span> <span class="nt" style="color: navy;">-f</span> sam <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: teal;">$nsortedbam</span>.sam.2</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"> assertEquals <span class="s2" style="color: #d14;">"ff5d66e6cd1cab4e8e6330f2829b7c41"</span> <span class="k" style="font-weight: 600;">$(</span><span class="nv" style="color: teal;"><span class="idiff left right">$</span>md5sum</span> <span class="nv" style="color: teal;">$nsortedbam</span>.sam.2 |cut <span class="nt" style="color: navy;">-c</span> 1-32<span class="k" style="font-weight: 600;">)</span></span>
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21
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># Test BAM</span></span>
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22
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="shell"> assertEquals <span class="s2" style="color: #d14;">"b5d64266e9544a656f0efbd0f8030b20"</span> <span class="k" style="font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">md5sum</span> <span class="nv" style="color: teal;">$nsortedbam</span> |cut <span class="nt" style="color: navy;">-c</span> 1-32<span class="k" style="font-weight: 600;">)</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"> assertEquals <span class="s2" style="color: #d14;">"b5d64266e9544a656f0efbd0f8030b20"</span> <span class="k" style="font-weight: 600;">$(</span><span class="nv" style="color: teal;"><span class="idiff left right">$</span>md5sum</span> <span class="nv" style="color: teal;">$nsortedbam</span> |cut <span class="nt" style="color: navy;">-c</span> 1-32<span class="k" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># ex1_header.sorted.bam with index</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> <span class="nb" style="color: #0086b3;">sort</span> <span class="nv" style="color: teal;">$outfn</span> <span class="nt" style="color: navy;">-o</span> <span class="nv" style="color: teal;">$sortedbam</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="shell"> assertEquals <span class="s2" style="color: #d14;">"b5d64266e9544a656f0efbd0f8030b20"</span> <span class="k" style="font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">md5sum</span> <span class="nv" style="color: teal;">$outfn</span> |cut <span class="nt" style="color: navy;">-c</span> 1-32<span class="k" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> index <span class="nv" style="color: teal;">$nsortedbam</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="shell"> assertEquals <span class="s2" style="color: #d14;">"aabb4fb319497dec1069028dd354eeda"</span> <span class="sb" style="color: #d14;">`</span><span class="idiff left">./bin/sambamba view </span><span class="nt" style="color: navy;"><span class="idiff">-f</span></span><span class="idiff"> unpack </span><span class="nv" style="color: teal;"><span class="idiff">$nsortedbam</span></span><span class="idiff right"> |</span>md5sum|cut <span class="nt" style="color: navy;">-c</span> 1-32<span class="sb" style="color: #d14;">`</span></span>
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28
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="shell"> assertEquals <span class="s2" style="color: #d14;">"68e19d0f1092e1f0429ba07b418d1d9f"</span> <span class="sb" style="color: #d14;">`</span><span class="idiff left">./bin/sambamba view </span><span class="nt" style="color: navy;"><span class="idiff">-f</span></span><span class="idiff"> unpack </span><span class="nv" style="color: teal;"><span class="idiff">$sortedbam</span></span><span class="idiff right"> |</span>md5sum|cut <span class="nt" style="color: navy;">-c</span> 1-32<span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> <span class="nv" style="color: teal;"><span class="idiff left">$opts</span></span><span class="idiff right"> </span><span class="nb" style="color: #0086b3;">sort</span> <span class="nv" style="color: teal;">$outfn</span> <span class="nt" style="color: navy;">-o</span> <span class="nv" style="color: teal;">$sortedbam</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell"> assertEquals <span class="s2" style="color: #d14;">"b5d64266e9544a656f0efbd0f8030b20"</span> <span class="k" style="font-weight: 600;">$(</span><span class="nv" style="color: teal;"><span class="idiff left right">$</span>md5sum</span> <span class="nv" style="color: teal;">$outfn</span> |cut <span class="nt" style="color: navy;">-c</span> 1-32<span class="k" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> <span class="nv" style="color: teal;"><span class="idiff left">$opts</span></span><span class="idiff right"> </span>index <span class="nv" style="color: teal;">$nsortedbam</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell"> assertEquals <span class="s2" style="color: #d14;">"aabb4fb319497dec1069028dd354eeda"</span> <span class="sb" style="color: #d14;">`</span><span class="nv" style="color: teal;"><span class="idiff left">$sambamba</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$opts</span></span><span class="idiff"> view </span><span class="nt" style="color: navy;"><span class="idiff">-f</span></span><span class="idiff"> unpack </span><span class="nv" style="color: teal;"><span class="idiff">$nsortedbam</span></span><span class="idiff"> |</span><span class="nv" style="color: teal;"><span class="idiff right">$</span>md5sum</span>|cut <span class="nt" style="color: navy;">-c</span> 1-32<span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell"> assertEquals <span class="s2" style="color: #d14;">"68e19d0f1092e1f0429ba07b418d1d9f"</span> <span class="sb" style="color: #d14;">`</span><span class="nv" style="color: teal;"><span class="idiff left">$sambamba</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$opts</span></span><span class="idiff"> view </span><span class="nt" style="color: navy;"><span class="idiff">-f</span></span><span class="idiff"> unpack </span><span class="nv" style="color: teal;"><span class="idiff">$sortedbam</span></span><span class="idiff"> |</span><span class="nv" style="color: teal;"><span class="idiff right">$</span>md5sum</span>|cut <span class="nt" style="color: navy;">-c</span> 1-32<span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="shell">testSubSample<span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="shell"> <span class="k" style="font-weight: 600;">return</span> <span class="c" style="color: #998; font-style: italic;"># not testing subsampling yet</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># bam file is part of BioD</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="shell"> <span class="nv" style="color: teal;">outfn</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">$outdir</span>/subsample.bam</span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> subsample <span class="nt" style="color: navy;">--type</span> fasthash <span class="nv" style="color: teal;">$outdir</span>/ex1_header.sorted.bam <span class="nt" style="color: navy;">--max-cov</span> 1000 <span class="nt" style="color: navy;">-o</span><span class="nv" style="color: teal;">$outfn</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: teal;">$outdir</span>/subsample.out</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> <span class="nv" style="color: teal;"><span class="idiff left">$opts</span></span><span class="idiff right"> </span>subsample <span class="nt" style="color: navy;">--type</span> fasthash <span class="nv" style="color: teal;">$outdir</span>/ex1_header.sorted.bam <span class="nt" style="color: navy;">--max-cov</span> 1000 <span class="nt" style="color: navy;">-o</span><span class="nv" style="color: teal;">$outfn</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: teal;">$outdir</span>/subsample.out</span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="shell"> assertEquals 0 <span class="nv" style="color: teal;">$?</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="shell"> assertEquals <span class="s2" style="color: #d14;">"ab4a69f0093674e9feec54afc2411059"</span> <span class="k" style="font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">md5sum</span> <span class="nv" style="color: teal;">$outfn</span> |cut <span class="nt" style="color: navy;">-c</span> 1-32<span class="k" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="shell"> assertEquals <span class="s2" style="color: #d14;">"ab4a69f0093674e9feec54afc2411059"</span> <span class="k" style="font-weight: 600;">$(</span><span class="nv" style="color: teal;"><span class="idiff left right">$</span>md5sum</span> <span class="nv" style="color: teal;">$outfn</span> |cut <span class="nt" style="color: navy;">-c</span> 1-32<span class="k" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># should be same as sorted bam</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="shell"> assertEquals <span class="s2" style="color: #d14;">"6e226f6acc8466115600d4de52ca8944"</span> <span class="sb" style="color: #d14;">`</span><span class="idiff left">./bin/sambamba view </span><span class="nt" style="color: navy;"><span class="idiff">-f</span></span><span class="idiff"> unpack </span><span class="nv" style="color: teal;"><span class="idiff">$outfn</span></span><span class="idiff right"> |</span>md5sum|cut <span class="nt" style="color: navy;">-c</span> 1-32<span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="shell"> assertEquals <span class="s2" style="color: #d14;">"6e226f6acc8466115600d4de52ca8944"</span> <span class="sb" style="color: #d14;">`</span><span class="nv" style="color: teal;"><span class="idiff left">$sambamba</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$opts</span></span><span class="idiff"> view </span><span class="nt" style="color: navy;"><span class="idiff">-f</span></span><span class="idiff"> unpack </span><span class="nv" style="color: teal;"><span class="idiff">$outfn</span></span><span class="idiff"> |</span><span class="nv" style="color: teal;"><span class="idiff right">$</span>md5sum</span>|cut <span class="nt" style="color: navy;">-c</span> 1-32<span class="sb" style="color: #d14;">`</span></span>
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40
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="shell"> <span class="nv" style="color: teal;">outfn</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">$outdir</span>/subsample2.bam</span>
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41
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> subsample <span class="nt" style="color: navy;">-r</span> <span class="nt" style="color: navy;">--type</span> fasthash <span class="nv" style="color: teal;">$outdir</span>/ex1_header.sorted.bam <span class="nt" style="color: navy;">--max-cov</span> 10 <span class="nt" style="color: navy;">-o</span><span class="nv" style="color: teal;">$outfn</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: teal;">$outdir</span>/subsample2.out</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> <span class="nv" style="color: teal;"><span class="idiff left">$opts</span></span><span class="idiff right"> </span>subsample <span class="nt" style="color: navy;">-r</span> <span class="nt" style="color: navy;">--type</span> fasthash <span class="nv" style="color: teal;">$outdir</span>/ex1_header.sorted.bam <span class="nt" style="color: navy;">--max-cov</span> 10 <span class="nt" style="color: navy;">-o</span><span class="nv" style="color: teal;">$outfn</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: teal;">$outdir</span>/subsample2.out</span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="shell"> assertEquals 0 <span class="nv" style="color: teal;">$?</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="shell"> assertEquals <span class="s2" style="color: #d14;">"4092fb75c87cde6efc47ff0a4dc443fb"</span> <span class="sb" style="color: #d14;">`</span><span class="idiff left">./bin/sambamba view </span><span class="nt" style="color: navy;"><span class="idiff">-f</span></span><span class="idiff"> unpack </span><span class="nv" style="color: teal;"><span class="idiff">$outfn</span></span><span class="idiff right"> |</span>md5sum|cut <span class="nt" style="color: navy;">-c</span> 1-32<span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="shell"> assertEquals <span class="s2" style="color: #d14;">"4092fb75c87cde6efc47ff0a4dc443fb"</span> <span class="sb" style="color: #d14;">`</span><span class="nv" style="color: teal;"><span class="idiff left">$sambamba</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$opts</span></span><span class="idiff"> view </span><span class="nt" style="color: navy;"><span class="idiff">-f</span></span><span class="idiff"> unpack </span><span class="nv" style="color: teal;"><span class="idiff">$outfn</span></span><span class="idiff"> |</span><span class="nv" style="color: teal;"><span class="idiff right">$</span>md5sum</span>|cut <span class="nt" style="color: navy;">-c</span> 1-32<span class="sb" style="color: #d14;">`</span></span>
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44
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="shell">testSortByName<span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="shell"> <span class="nv" style="color: teal;">outfn</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">$outdir</span>/ex1_header.nsorted.sam</span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># use very tiny buffer of 200K so that multithreading is used</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> <span class="nb" style="color: #0086b3;">sort</span> <span class="nt" style="color: navy;">-t2</span> <span class="nt" style="color: navy;">-n</span> <span class="nv" style="color: teal;">$sortedbam</span> <span class="nt" style="color: navy;">-o</span> <span class="nv" style="color: teal;">$nsortedbam</span> <span class="nt" style="color: navy;">-m</span> 200K</span>
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50
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> view <span class="nt" style="color: navy;">-t2</span> <span class="nv" style="color: teal;">$nsortedbam</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: teal;">$outfn</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> <span class="nv" style="color: teal;"><span class="idiff left">$opts</span></span><span class="idiff right"> </span><span class="nb" style="color: #0086b3;">sort</span> <span class="nt" style="color: navy;">-t2</span> <span class="nt" style="color: navy;">-n</span> <span class="nv" style="color: teal;">$sortedbam</span> <span class="nt" style="color: navy;">-o</span> <span class="nv" style="color: teal;">$nsortedbam</span> <span class="nt" style="color: navy;">-m</span> 200K</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> <span class="nv" style="color: teal;"><span class="idiff left">$opts</span></span><span class="idiff right"> </span>view <span class="nt" style="color: navy;">-t2</span> <span class="nv" style="color: teal;">$nsortedbam</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: teal;">$outfn</span></span>
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51
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="shell"> assertEquals <span class="s2" style="color: #d14;">"3270"</span> <span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">wc</span> <span class="nt" style="color: navy;">-l</span> < <span class="nv" style="color: teal;">$outfn</span><span class="sb" style="color: #d14;">`</span></span>
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56
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">cat</span> <span class="nv" style="color: teal;">$outfn</span> | <span class="nb" style="color: #0086b3;">cut</span> <span class="nt" style="color: navy;">-f1</span> | <span class="nv" style="color: teal;">LC_ALL</span><span class="o" style="font-weight: 600;">=</span>C <span class="nb" style="color: #0086b3;">sort</span> <span class="nt" style="color: navy;">-c</span></span>
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53
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="shell"> assertEquals 0 <span class="nv" style="color: teal;">$?</span></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">@@ -55,137 +59,144 @@ testSortByName() {</td>
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59
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="shell">testSortByCoordinate<span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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57
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="shell"> <span class="nv" style="color: teal;">outfn</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">$outdir</span>/ex1_header.sorted2.bam</span>
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58
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> <span class="nb" style="color: #0086b3;">sort</span> <span class="nt" style="color: navy;">-t2</span> <span class="nt" style="color: navy;">-m</span> 300K <span class="nv" style="color: teal;">$nsortedbam</span> <span class="nt" style="color: navy;">-o</span> <span class="nv" style="color: teal;">$outfn</span></span>
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59
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="shell"> <span class="nv" style="color: teal;"><span class="idiff left right">$sambamba</span></span> index <span class="nt" style="color: navy;">-t2</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> <span class="nv" style="color: teal;"><span class="idiff left">$opts</span></span><span class="idiff right"> </span><span class="nb" style="color: #0086b3;">sort</span> <span class="nt" style="color: navy;">-t2</span> <span class="nt" style="color: navy;">-m</span> 300K <span class="nv" style="color: teal;">$nsortedbam</span> <span class="nt" style="color: navy;">-o</span> <span class="nv" style="color: teal;">$outfn</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"><span class="idiff left right"># $sambamba $opts</span> index -t2</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="shell"> assertEquals 0 <span class="nv" style="color: teal;">$?</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> view <span class="nt" style="color: navy;">-t2</span> <span class="nv" style="color: teal;">$outfn</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: teal;">$outfn</span>.sam</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> <span class="nv" style="color: teal;"><span class="idiff left">$opts</span></span><span class="idiff right"> </span>view <span class="nt" style="color: navy;">-t2</span> <span class="nv" style="color: teal;">$outfn</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: teal;">$outfn</span>.sam</span>
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62
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66
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># check sorted with cat output/ex1_header.sorted2.bam.sam |awk '{print $3 " " $4}'|less</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="shell"> assertEquals <span class="s2" style="color: #d14;">"d92c51b9e067590d7d5a18a0bdbbe0cc"</span> <span class="sb" style="color: #d14;">`</span><span class="idiff left">./bin/sambamba view </span><span class="nt" style="color: navy;"><span class="idiff">-f</span></span><span class="idiff"> unpack </span><span class="nv" style="color: teal;"><span class="idiff">$outfn</span></span><span class="idiff right"> |</span>md5sum|cut <span class="nt" style="color: navy;">-c</span> 1-32<span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="shell"> assertEquals <span class="s2" style="color: #d14;">"d92c51b9e067590d7d5a18a0bdbbe0cc"</span> <span class="sb" style="color: #d14;">`</span><span class="nv" style="color: teal;"><span class="idiff left">$sambamba</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$opts</span></span><span class="idiff"> view </span><span class="nt" style="color: navy;"><span class="idiff">-f</span></span><span class="idiff"> unpack </span><span class="nv" style="color: teal;"><span class="idiff">$outfn</span></span><span class="idiff"> |</span><span class="nv" style="color: teal;"><span class="idiff right">$</span>md5sum</span>|cut <span class="nt" style="color: navy;">-c</span> 1-32<span class="sb" style="color: #d14;">`</span></span>
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64
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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69
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="shell">testSlice<span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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67
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> slice <span class="nv" style="color: teal;">$sortedbam</span> chr1 <span class="nt" style="color: navy;">-o</span> /dev/null</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> <span class="nv" style="color: teal;"><span class="idiff left">$opts</span></span><span class="idiff right"> </span>slice <span class="nv" style="color: teal;">$sortedbam</span> chr1 <span class="nt" style="color: navy;">-o</span> /dev/null</span>
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68
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72
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="shell"> assertEquals 0 <span class="nv" style="color: teal;">$?</span></span>
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69
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73
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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70
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="shell"></span>
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71
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75
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="shell">testSliceMultipleRegions<span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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72
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> slice <span class="nb" style="color: #0086b3;">test</span>/issue_204.bam 2:166860000-166870000 2:166860000-166870000 |<span class="se" style="color: #d14;">\</span></span>
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73
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> view <span class="nt" style="color: navy;">-c</span> /dev/stdin <span class="o" style="font-weight: 600;">></span> /dev/null</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> <span class="nv" style="color: teal;"><span class="idiff left">$opts</span></span><span class="idiff right"> </span>slice <span class="nb" style="color: #0086b3;">test</span>/issue_204.bam 2:166860000-166870000 2:166860000-166870000 |<span class="se" style="color: #d14;">\</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> <span class="nv" style="color: teal;"><span class="idiff left">$opts</span></span><span class="idiff right"> </span>view <span class="nt" style="color: navy;">-c</span> /dev/stdin <span class="o" style="font-weight: 600;">></span> /dev/null</span>
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74
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78
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="shell"> assertEquals 0 <span class="nv" style="color: teal;">$?</span></span>
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75
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79
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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76
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80
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="shell"></span>
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77
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81
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="shell">testSliceMultipleRegionsBed<span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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78
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="shell"> assertEquals <span class="s2" style="color: #d14;">"156"</span> <span class="sb" style="color: #d14;">`</span><span class="nv" style="color: teal;">$sambamba</span> slice <span class="nt" style="color: navy;">-L</span> <span class="nb" style="color: #0086b3;">test</span>/chr2_chr3_test_region.bed <span class="nb" style="color: #0086b3;">test</span>/issue_204.bam |<span class="se" style="color: #d14;">\</span></span>
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79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> view <span class="nt" style="color: navy;">-c</span> /dev/stdin<span class="sb" style="color: #d14;">`</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="shell"> assertEquals <span class="s2" style="color: #d14;">"156"</span> <span class="sb" style="color: #d14;">`</span><span class="nv" style="color: teal;">$sambamba</span> <span class="nv" style="color: teal;"><span class="idiff left">$opts</span></span><span class="idiff right"> </span>slice <span class="nt" style="color: navy;">-L</span> <span class="nb" style="color: #0086b3;">test</span>/chr2_chr3_test_region.bed <span class="nb" style="color: #0086b3;">test</span>/issue_204.bam |<span class="se" style="color: #d14;">\</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> <span class="nv" style="color: teal;"><span class="idiff left">$opts</span></span><span class="idiff right"> </span>view <span class="nt" style="color: navy;">-c</span> /dev/stdin<span class="sb" style="color: #d14;">`</span></span>
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80
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84
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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81
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85
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="shell"></span>
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82
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86
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="shell">testView<span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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83
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="shell"> assertEquals <span class="s2" style="color: #d14;">"1806"</span> <span class="sb" style="color: #d14;">`</span><span class="nv" style="color: teal;">$sambamba</span> view <span class="nt" style="color: navy;">-c</span> <span class="nv" style="color: teal;">$sortedbam</span> chr2<span class="sb" style="color: #d14;">`</span></span>
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84
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="shell"> assertEquals <span class="s2" style="color: #d14;">"1464"</span> <span class="sb" style="color: #d14;">`</span><span class="nv" style="color: teal;">$sambamba</span> view <span class="nt" style="color: navy;">-c</span> <span class="nv" style="color: teal;">$sortedbam</span> chr1<span class="sb" style="color: #d14;">`</span></span>
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<td class="diff-line-num old old_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
85
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="shell"> assertEquals <span class="s2" style="color: #d14;">"0"</span> <span class="sb" style="color: #d14;">`</span><span class="nv" style="color: teal;">$sambamba</span> view <span class="nt" style="color: navy;">-c</span> <span class="nv" style="color: teal;">$sortedbam</span> <span class="s1" style="color: #d14;">'*'</span><span class="sb" style="color: #d14;">`</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="shell"> assertEquals <span class="s2" style="color: #d14;">"1806"</span> <span class="sb" style="color: #d14;">`</span><span class="nv" style="color: teal;">$sambamba</span> <span class="nv" style="color: teal;"><span class="idiff left">$opts</span></span><span class="idiff right"> </span>view <span class="nt" style="color: navy;">-c</span> <span class="nv" style="color: teal;">$sortedbam</span> chr2<span class="sb" style="color: #d14;">`</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="shell"> assertEquals <span class="s2" style="color: #d14;">"1464"</span> <span class="sb" style="color: #d14;">`</span><span class="nv" style="color: teal;">$sambamba</span> <span class="nv" style="color: teal;"><span class="idiff left">$opts</span></span><span class="idiff right"> </span>view <span class="nt" style="color: navy;">-c</span> <span class="nv" style="color: teal;">$sortedbam</span> chr1<span class="sb" style="color: #d14;">`</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="shell"> assertEquals <span class="s2" style="color: #d14;">"0"</span> <span class="sb" style="color: #d14;">`</span><span class="nv" style="color: teal;">$sambamba</span> <span class="nv" style="color: teal;"><span class="idiff left">$opts</span></span><span class="idiff right"> </span>view <span class="nt" style="color: navy;">-c</span> <span class="nv" style="color: teal;">$sortedbam</span> <span class="s1" style="color: #d14;">'*'</span><span class="sb" style="color: #d14;">`</span></span>
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86
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90
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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87
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91
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="shell"></span>
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88
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92
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="shell">testOverwriteProtection<span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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89
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> view <span class="nv" style="color: teal;">$nsortedbam</span> <span class="nt" style="color: navy;">-f</span> bam <span class="nt" style="color: navy;">-o</span> ./<span class="nv" style="color: teal;">$nsortedbam</span> 2>/dev/null</span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> <span class="nv" style="color: teal;"><span class="idiff left">$opts</span></span><span class="idiff right"> </span>view <span class="nv" style="color: teal;">$nsortedbam</span> <span class="nt" style="color: navy;">-f</span> bam <span class="nt" style="color: navy;">-o</span> ./<span class="nv" style="color: teal;">$nsortedbam</span> 2>/dev/null</span>
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90
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94
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="shell"> assertNotSame 0 <span class="nv" style="color: teal;">$?</span></span>
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91
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> merge <span class="nv" style="color: teal;">$sortedbam</span> <span class="nv" style="color: teal;">$sortedbam</span> <span class="nv" style="color: teal;">$sortedbam</span> 2>/dev/null</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> <span class="nv" style="color: teal;"><span class="idiff left">$opts</span></span><span class="idiff right"> </span>merge <span class="nv" style="color: teal;">$sortedbam</span> <span class="nv" style="color: teal;">$sortedbam</span> <span class="nv" style="color: teal;">$sortedbam</span> 2>/dev/null</span>
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92
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96
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="shell"> assertNotSame 0 <span class="nv" style="color: teal;">$?</span></span>
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93
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> <span class="nb" style="color: #0086b3;">sort</span> <span class="nt" style="color: navy;">-m</span> 50M <span class="nv" style="color: teal;">$nsortedbam</span> <span class="nt" style="color: navy;">-o</span> ./bin/../<span class="nv" style="color: teal;">$nsortedbam</span> 2>/dev/null</span>
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<td class="diff-line-num new new_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> <span class="nv" style="color: teal;"><span class="idiff left">$opts</span></span><span class="idiff right"> </span><span class="nb" style="color: #0086b3;">sort</span> <span class="nt" style="color: navy;">-m</span> 50M <span class="nv" style="color: teal;">$nsortedbam</span> <span class="nt" style="color: navy;">-o</span> ./bin/../<span class="nv" style="color: teal;">$nsortedbam</span> 2>/dev/null</span>
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94
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98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="shell"> assertNotSame 0 <span class="nv" style="color: teal;">$?</span></span>
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95
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> markdup <span class="nv" style="color: teal;">$nsortedbam</span> ./bin/../<span class="nv" style="color: teal;">$nsortedbam</span> 2>/dev/null</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> <span class="nv" style="color: teal;"><span class="idiff left">$opts</span></span><span class="idiff right"> </span>markdup <span class="nv" style="color: teal;">$nsortedbam</span> ./bin/../<span class="nv" style="color: teal;">$nsortedbam</span> 2>/dev/null</span>
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96
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100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="shell"> assertNotSame 0 <span class="nv" style="color: teal;">$?</span></span>
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<td class="diff-line-num old old_line" data-linenumber="97" 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">
97
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<td class="diff-line-num new_line old" data-linenumber="101" 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="LC97" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> slice <span class="nv" style="color: teal;">$nsortedbam</span> chr1 <span class="nt" style="color: navy;">-o</span> ./bin/../<span class="nv" style="color: teal;">$nsortedbam</span> 2>/dev/null</span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> <span class="nv" style="color: teal;"><span class="idiff left">$opts</span></span><span class="idiff right"> </span>slice <span class="nv" style="color: teal;">$nsortedbam</span> chr1 <span class="nt" style="color: navy;">-o</span> ./bin/../<span class="nv" style="color: teal;">$nsortedbam</span> 2>/dev/null</span>
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98
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102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="shell"> assertNotSame 0 <span class="nv" style="color: teal;">$?</span></span>
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99
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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100
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104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="shell"></span>
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101
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105
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="shell">testSortingEmptyFile<span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> view <span class="nv" style="color: teal;">$sortedbam</span> <span class="nt" style="color: navy;">-f</span> bam <span class="nt" style="color: navy;">-F</span> <span class="s2" style="color: #d14;">"ref_id > 3"</span> <span class="nt" style="color: navy;">-o</span> <span class="nv" style="color: teal;">$outdir</span>/empty.bam 2>/dev/null</span>
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103
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> <span class="nb" style="color: #0086b3;">sort</span> <span class="nt" style="color: navy;">-m</span> 50M <span class="nv" style="color: teal;">$outdir</span>/empty.bam <span class="nt" style="color: navy;">-o</span> <span class="nv" style="color: teal;">$outdir</span>/empty2.bam 2>/dev/null</span>
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104
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="shell"> assertEquals <span class="s2" style="color: #d14;">"0"</span> <span class="sb" style="color: #d14;">`</span><span class="nv" style="color: teal;">$sambamba</span> view <span class="nt" style="color: navy;">-c</span> <span class="nv" style="color: teal;">$outdir</span>/empty2.bam<span class="sb" style="color: #d14;">`</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> <span class="nv" style="color: teal;"><span class="idiff left">$opts</span></span><span class="idiff right"> </span>view <span class="nv" style="color: teal;">$sortedbam</span> <span class="nt" style="color: navy;">-f</span> bam <span class="nt" style="color: navy;">-F</span> <span class="s2" style="color: #d14;">"ref_id > 3"</span> <span class="nt" style="color: navy;">-o</span> <span class="nv" style="color: teal;">$outdir</span>/empty.bam 2>/dev/null</span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> <span class="nv" style="color: teal;"><span class="idiff left">$opts</span></span><span class="idiff right"> </span><span class="nb" style="color: #0086b3;">sort</span> <span class="nt" style="color: navy;">-m</span> 50M <span class="nv" style="color: teal;">$outdir</span>/empty.bam <span class="nt" style="color: navy;">-o</span> <span class="nv" style="color: teal;">$outdir</span>/empty2.bam 2>/dev/null</span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="shell"> assertEquals <span class="s2" style="color: #d14;">"0"</span> <span class="sb" style="color: #d14;">`</span><span class="nv" style="color: teal;">$sambamba</span> <span class="nv" style="color: teal;"><span class="idiff left">$opts</span></span><span class="idiff right"> </span>view <span class="nt" style="color: navy;">-c</span> <span class="nv" style="color: teal;">$outdir</span>/empty2.bam<span class="sb" style="color: #d14;">`</span></span>
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105
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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106
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110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="shell"></span>
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107
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111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="shell">testMarkdupEmptyFile<span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> view <span class="nv" style="color: teal;">$sortedbam</span> <span class="nt" style="color: navy;">-f</span> bam <span class="nt" style="color: navy;">-F</span> <span class="s2" style="color: #d14;">"ref_id > 3"</span> <span class="nt" style="color: navy;">-o</span> <span class="nv" style="color: teal;">$outdir</span>/empty.bam 2>/dev/null</span>
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<td class="diff-line-num old old_line" data-linenumber="109" 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">
109
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> markdup <span class="nv" style="color: teal;">$outdir</span>/empty.bam <span class="nv" style="color: teal;">$outdir</span>/empty.dedup.bam 2>/dev/null</span>
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110
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="shell"> assertEquals <span class="s2" style="color: #d14;">"0"</span> <span class="sb" style="color: #d14;">`</span><span class="nv" style="color: teal;">$sambamba</span> view <span class="nt" style="color: navy;">-c</span> <span class="nv" style="color: teal;">$outdir</span>/empty.dedup.bam<span class="sb" style="color: #d14;">`</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> <span class="nv" style="color: teal;"><span class="idiff left">$opts</span></span><span class="idiff right"> </span>view <span class="nv" style="color: teal;">$sortedbam</span> <span class="nt" style="color: navy;">-f</span> bam <span class="nt" style="color: navy;">-F</span> <span class="s2" style="color: #d14;">"ref_id > 3"</span> <span class="nt" style="color: navy;">-o</span> <span class="nv" style="color: teal;">$outdir</span>/empty.bam 2>/dev/null</span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> <span class="nv" style="color: teal;"><span class="idiff left">$opts</span></span><span class="idiff right"> </span>markdup <span class="nv" style="color: teal;">$outdir</span>/empty.bam <span class="nv" style="color: teal;">$outdir</span>/empty.dedup.bam 2>/dev/null</span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="shell"> assertEquals <span class="s2" style="color: #d14;">"0"</span> <span class="sb" style="color: #d14;">`</span><span class="nv" style="color: teal;">$sambamba</span> <span class="nv" style="color: teal;"><span class="idiff left">$opts</span></span><span class="idiff right"> </span>view <span class="nt" style="color: navy;">-c</span> <span class="nv" style="color: teal;">$outdir</span>/empty.dedup.bam<span class="sb" style="color: #d14;">`</span></span>
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111
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115
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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112
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116
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="shell"></span>
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<td class="diff-line-num old_line" data-linenumber="113" 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">
113
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117
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="shell">testCramWriting<span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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114
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> view <span class="nt" style="color: navy;">-S</span> htslib/test/c1<span class="se" style="color: #d14;">\#</span>pad2.sam <span class="nt" style="color: navy;">-T</span> htslib/test/c1.fa <span class="nt" style="color: navy;">-f</span> cram <span class="nt" style="color: navy;">-o</span> <span class="nv" style="color: teal;">$outdir</span>/c1_pad2.cram</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="shell"> <span class="nv" style="color: teal;">$sambamba</span> <span class="nv" style="color: teal;"><span class="idiff left">$opts</span></span><span class="idiff right"> </span>view <span class="nt" style="color: navy;">-S</span> htslib/test/c1<span class="se" style="color: #d14;">\#</span>pad2.sam <span class="nt" style="color: navy;">-T</span> htslib/test/c1.fa <span class="nt" style="color: navy;">-f</span> cram <span class="nt" style="color: navy;">-o</span> <span class="nv" style="color: teal;">$outdir</span>/c1_pad2.cram</span>
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115
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<td class="diff-line-num new_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
119
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="shell"> assertEquals 0 <span class="nv" style="color: teal;">$?</span></span>
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<td class="diff-line-num old_line" data-linenumber="116" 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">
116
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120
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="117" 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">
117
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121
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="shell"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="118" 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">
118
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<td class="diff-line-num new_line" data-linenumber="122" 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">
122
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="shell">testCramReading<span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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119
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> view <span class="nt" style="color: navy;">-C</span> <span class="nv" style="color: teal;">$outdir</span>/c1_pad2.cram <span class="o" style="font-weight: 600;">></span>/dev/null</span>
</pre>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> <span class="nv" style="color: teal;"><span class="idiff left">$opts</span></span><span class="idiff right"> </span>view <span class="nt" style="color: navy;">-C</span> <span class="nv" style="color: teal;">$outdir</span>/c1_pad2.cram <span class="o" style="font-weight: 600;">></span>/dev/null</span>
</pre>
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120
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<td class="diff-line-num new_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
124
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="shell"> assertEquals 0 <span class="nv" style="color: teal;">$?</span></span>
</pre>
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121
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<td class="diff-line-num new_line" data-linenumber="125" 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">
125
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
</pre>
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122
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126
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="shell"></span>
</pre>
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123
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127
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="shell">testIndexUsage<span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
</pre>
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124
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">rm</span> <span class="k" style="font-weight: 600;"><span class="idiff left">*</span></span><span class="idiff">.bai </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">rm </span></span>c1_<span class="k" style="font-weight: 600;">*</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="125" 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">
125
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<td class="diff-line-num new_line old" data-linenumber="128" 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="LC125" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> view <span class="nt" style="color: navy;">-S</span> htslib/test/c1<span class="se" style="color: #d14;">\#</span>pad2.sam <span class="nt" style="color: navy;">-T</span> htslib/test/c1.fa <span class="nt" style="color: navy;">-f</span> cram <span class="nt" style="color: navy;">-o</span> <span class="nv" style="color: teal;">$outdir</span>/c1_pad2.cram <span class="o" style="font-weight: 600;">&&</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="126" 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">
126
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<td class="diff-line-num new_line old" data-linenumber="128" 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="LC126" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> index <span class="nt" style="color: navy;">-C</span> <span class="nv" style="color: teal;">$outdir</span>/c1_pad2.cram <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">test</span> <span class="nt" style="color: navy;">-e</span> <span class="nv" style="color: teal;">$outdir</span>/c1_pad2.cram.crai<span class="p">;</span> assertEquals 0 <span class="nv" style="color: teal;">$?</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="127" 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">
127
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<td class="diff-line-num new_line old" data-linenumber="128" 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="LC127" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> index <span class="nt" style="color: navy;">-C</span> <span class="nv" style="color: teal;">$outdir</span>/c1_pad2.cram <span class="nv" style="color: teal;">$outdir</span>/c1_cram_index <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">test</span> <span class="nt" style="color: navy;">-e</span> <span class="nv" style="color: teal;">$outdir</span>/c1_cram_index.crai<span class="p">;</span> assertEquals 0 <span class="nv" style="color: teal;">$?</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
128
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> index <span class="nv" style="color: teal;">$sortedbam</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">test</span> <span class="nt" style="color: navy;">-e</span> <span class="nv" style="color: teal;">$sortedbam</span>.bai<span class="p">;</span> assertEquals 0 <span class="nv" style="color: teal;">$?</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
129
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<td class="diff-line-num new_line old" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> index <span class="nv" style="color: teal;">$sortedbam</span> <span class="nv" style="color: teal;">$outdir</span>/ex1_header.sorted.bai <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">test</span> <span class="nt" style="color: navy;">-e</span> <span class="nv" style="color: teal;">$outdir</span>/ex1_header.sorted.bai<span class="p">;</span> assertEquals 0 <span class="nv" style="color: teal;">$?</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="130" style="width: 35px; color: rgba(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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<pre style="margin: 0;">+<span id="LC128" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: navy;"><span class="idiff left">-f</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$outdir</span></span><span class="idiff">/</span><span class="k" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff">.bai </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">rm</span></span><span class="idiff"> </span><span class="nt" style="color: navy;"><span class="idiff">-f</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$outdir</span></span><span class="idiff right">/</span>c1_<span class="k" style="font-weight: 600;">*</span></span>
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<td class="diff-line-num new old_line" data-linenumber="130" style="width: 35px; color: rgba(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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<pre style="margin: 0;">+<span id="LC129" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> <span class="nv" style="color: teal;"><span class="idiff left">$opts</span></span><span class="idiff right"> </span>view <span class="nt" style="color: navy;">-S</span> htslib/test/c1<span class="se" style="color: #d14;">\#</span>pad2.sam <span class="nt" style="color: navy;">-T</span> htslib/test/c1.fa <span class="nt" style="color: navy;">-f</span> cram <span class="nt" style="color: navy;">-o</span> <span class="nv" style="color: teal;">$outdir</span>/c1_pad2.cram <span class="o" style="font-weight: 600;">&&</span></span>
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<td class="diff-line-num new old_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> <span class="nv" style="color: teal;"><span class="idiff left">$opts</span></span><span class="idiff right"> </span>index <span class="nt" style="color: navy;">-C</span> <span class="nv" style="color: teal;">$outdir</span>/c1_pad2.cram <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">test</span> <span class="nt" style="color: navy;">-e</span> <span class="nv" style="color: teal;">$outdir</span>/c1_pad2.cram.crai<span class="p">;</span> assertEquals 0 <span class="nv" style="color: teal;">$?</span></span>
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<td class="diff-line-num new old_line" data-linenumber="130" style="width: 35px; color: rgba(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="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> <span class="nv" style="color: teal;"><span class="idiff left">$opts</span></span><span class="idiff right"> </span>index <span class="nt" style="color: navy;">-C</span> <span class="nv" style="color: teal;">$outdir</span>/c1_pad2.cram <span class="nv" style="color: teal;">$outdir</span>/c1_cram_index <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">test</span> <span class="nt" style="color: navy;">-e</span> <span class="nv" style="color: teal;">$outdir</span>/c1_cram_index.crai<span class="p">;</span> assertEquals 0 <span class="nv" style="color: teal;">$?</span></span>
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<td class="diff-line-num new old_line" data-linenumber="130" style="width: 35px; color: rgba(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="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> <span class="nv" style="color: teal;"><span class="idiff left">$opts</span></span><span class="idiff right"> </span>index <span class="nv" style="color: teal;">$sortedbam</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">test</span> <span class="nt" style="color: navy;">-e</span> <span class="nv" style="color: teal;">$sortedbam</span>.bai<span class="p">;</span> assertEquals 0 <span class="nv" style="color: teal;">$?</span></span>
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<td class="diff-line-num new old_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> <span class="nv" style="color: teal;"><span class="idiff left">$opts</span></span><span class="idiff right"> </span>index <span class="nv" style="color: teal;">$sortedbam</span> <span class="nv" style="color: teal;">$outdir</span>/ex1_header.sorted.bai <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">test</span> <span class="nt" style="color: navy;">-e</span> <span class="nv" style="color: teal;">$outdir</span>/ex1_header.sorted.bai<span class="p">;</span> assertEquals 0 <span class="nv" style="color: teal;">$?</span></span>
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<td class="diff-line-num old_line" data-linenumber="130" 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">
130
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<td class="diff-line-num new_line" data-linenumber="134" 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">
134
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="131" 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">
131
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<td class="diff-line-num new_line" data-linenumber="135" 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">
135
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="shell"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="132" 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">
132
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<td class="diff-line-num new_line" data-linenumber="136" 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">
136
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="shell">testIssue193<span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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133
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<td class="diff-line-num new_line" data-linenumber="137" 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">
137
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: navy;">-f</span> <span class="nv" style="color: teal;">$outdir</span>/output_193.txt</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="134" 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">
134
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<td class="diff-line-num new_line old" data-linenumber="138" 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="LC134" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> depth base <span class="nb" style="color: #0086b3;">test</span>/issue_193.bam <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: teal;">$outdir</span>/output_193.txt 2>/dev/null</span>
</pre>
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<td class="diff-line-num new old_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">
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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="shell"> <span class="nv" style="color: teal;">$sambamba</span> <span class="nv" style="color: teal;"><span class="idiff left">$opts</span></span><span class="idiff right"> </span>depth base <span class="nb" style="color: #0086b3;">test</span>/issue_193.bam <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: teal;">$outdir</span>/output_193.txt 2>/dev/null</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
135
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<td class="diff-line-num new_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
139
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="shell"> diff <span class="nt" style="color: navy;">-q</span> <span class="nv" style="color: teal;">$outdir</span>/output_193.txt <span class="nb" style="color: #0086b3;">test</span>/issue_193_expected_output.txt</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="136" 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">
136
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<td class="diff-line-num new_line" data-linenumber="140" 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">
140
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="shell"> assertEquals 0 <span class="nv" style="color: teal;">$?</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="137" 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">
137
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<td class="diff-line-num new_line" data-linenumber="141" 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">
141
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="138" 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">
138
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<td class="diff-line-num new_line" data-linenumber="142" 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">
142
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="shell"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="139" 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">
139
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<td class="diff-line-num new_line" data-linenumber="143" 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">
143
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="shell">testIssue204<span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="140" 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">
140
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<td class="diff-line-num new_line" data-linenumber="144" 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">
144
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: navy;">-f</span> <span class="nv" style="color: teal;">$outdir</span>/output_204.txt</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="141" 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">
141
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<td class="diff-line-num new_line old" data-linenumber="145" 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="LC141" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> index <span class="nb" style="color: #0086b3;">test</span>/issue_204.bam</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
142
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<td class="diff-line-num new_line old" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> depth region <span class="nb" style="color: #0086b3;">test</span>/issue_204.bam <span class="nt" style="color: navy;">-L</span> 2:166868600-166868813 <span class="nt" style="color: navy;">-T</span> 15 <span class="nt" style="color: navy;">-T</span> 20 <span class="nt" style="color: navy;">-T</span> 25 <span class="nt" style="color: navy;">-m</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: teal;">$outdir</span>/output_204.txt 2>/dev/null</span>
</pre>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> <span class="nv" style="color: teal;"><span class="idiff left">$opts</span></span><span class="idiff right"> </span>index <span class="nb" style="color: #0086b3;">test</span>/issue_204.bam</span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> <span class="nv" style="color: teal;"><span class="idiff left">$opts</span></span><span class="idiff right"> </span>depth region <span class="nb" style="color: #0086b3;">test</span>/issue_204.bam <span class="nt" style="color: navy;">-L</span> 2:166868600-166868813 <span class="nt" style="color: navy;">-T</span> 15 <span class="nt" style="color: navy;">-T</span> 20 <span class="nt" style="color: navy;">-T</span> 25 <span class="nt" style="color: navy;">-m</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: teal;">$outdir</span>/output_204.txt 2>/dev/null</span>
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143
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147
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="shell"> diff <span class="nt" style="color: navy;">-q</span> <span class="nv" style="color: teal;">$outdir</span>/output_204.txt <span class="nb" style="color: #0086b3;">test</span>/issue_204_expected_output.txt</span>
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144
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148
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="shell"> assertEquals 0 <span class="nv" style="color: teal;">$?</span></span>
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145
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149
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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146
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150
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="shell"></span>
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147
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151
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="shell">testIssue206<span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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148
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> markdup <span class="nv" style="color: teal;">$sortedbam</span> <span class="nv" style="color: teal;">$outdir</span>/ex1_header.dedup.bam 2>/dev/null</span>
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149
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> view <span class="nt" style="color: navy;">-H</span> <span class="nv" style="color: teal;">$outdir</span>/ex1_header.dedup.bam | <span class="nb" style="color: #0086b3;">grep</span> <span class="s1" style="color: #d14;">'@PG'</span> | <span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: navy;">-q</span> <span class="s1" style="color: #d14;">'sambamba'</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> <span class="nv" style="color: teal;"><span class="idiff left">$opts</span></span><span class="idiff right"> </span>markdup <span class="nv" style="color: teal;">$sortedbam</span> <span class="nv" style="color: teal;">$outdir</span>/ex1_header.dedup.bam 2>/dev/null</span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> <span class="nv" style="color: teal;"><span class="idiff left">$opts</span></span><span class="idiff right"> </span>view <span class="nt" style="color: navy;">-H</span> <span class="nv" style="color: teal;">$outdir</span>/ex1_header.dedup.bam | <span class="nb" style="color: #0086b3;">grep</span> <span class="s1" style="color: #d14;">'@PG'</span> | <span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: navy;">-q</span> <span class="s1" style="color: #d14;">'sambamba'</span></span>
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150
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154
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="shell"> assertEquals 0 <span class="nv" style="color: teal;">$?</span></span>
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<td class="diff-line-num old_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
151
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<td class="diff-line-num new_line" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
155
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="shell"></span>
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<td class="diff-line-num old old_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
152
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> view <span class="nv" style="color: teal;">$sortedbam</span> <span class="nt" style="color: navy;">-f</span> bam <span class="nt" style="color: navy;">-o</span> <span class="nv" style="color: teal;">$outdir</span>/ex1_header.filtered.bam <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> <span class="nv" style="color: teal;"><span class="idiff left">$opts</span></span><span class="idiff right"> </span>view <span class="nv" style="color: teal;">$sortedbam</span> <span class="nt" style="color: navy;">-f</span> bam <span class="nt" style="color: navy;">-o</span> <span class="nv" style="color: teal;">$outdir</span>/ex1_header.filtered.bam <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num old_line" data-linenumber="153" 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">
153
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<td class="diff-line-num new_line" data-linenumber="157" 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">
157
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="shell"> <span class="nt" style="color: navy;">-F</span> <span class="s2" style="color: #d14;">"supplementary or secondary_alignment"</span></span>
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<td class="diff-line-num old_line" data-linenumber="154" 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">
154
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158
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># skip failing test - filtered bam is not complete</span></span>
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155
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<td class="diff-line-num new_line old" data-linenumber="159" 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="LC155" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># $sambamba view -H $outdir/ex1_header.filtered.bam | grep '@PG' | grep -q 'secondary'</span></span>
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<td class="diff-line-num new new_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># $sambamba <span class="idiff left right">$opts </span>view -H $outdir/ex1_header.filtered.bam | grep '@PG' | grep -q 'secondary'</span></span>
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156
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160
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="shell"> assertEquals 0 <span class="nv" style="color: teal;">$?</span></span>
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157
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161
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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158
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162
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="shell"></span>
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<td class="diff-line-num old_line" data-linenumber="159" 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">
159
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<td class="diff-line-num new_line" data-linenumber="163" 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">
163
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="shell">testIssue225<span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="160" 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">
160
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> index <span class="nb" style="color: #0086b3;">test</span>/issue225.bam</span>
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<td class="diff-line-num old old_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
161
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<td class="diff-line-num new_line old" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> depth base <span class="nt" style="color: navy;">-c</span> 1 <span class="nb" style="color: #0086b3;">test</span>/issue225.bam <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: teal;">$outdir</span>/depth_base_225_1.txt 2>/dev/null</span>
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<td class="diff-line-num new old_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> <span class="nv" style="color: teal;"><span class="idiff left">$opts</span></span><span class="idiff right"> </span>index <span class="nb" style="color: #0086b3;">test</span>/issue225.bam</span>
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<td class="diff-line-num new old_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> <span class="nv" style="color: teal;"><span class="idiff left">$opts</span></span><span class="idiff right"> </span>depth base <span class="nt" style="color: navy;">-c</span> 1 <span class="nb" style="color: #0086b3;">test</span>/issue225.bam <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: teal;">$outdir</span>/depth_base_225_1.txt 2>/dev/null</span>
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<td class="diff-line-num old_line" data-linenumber="162" 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">
162
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<td class="diff-line-num new_line" data-linenumber="166" 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">
166
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="shell"> diff <span class="nt" style="color: navy;">-q</span> <span class="nv" style="color: teal;">$outdir</span>/depth_base_225_1.txt <span class="nb" style="color: #0086b3;">test</span>/issue225.out</span>
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<td class="diff-line-num old_line" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
163
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<td class="diff-line-num new_line" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
167
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="shell"> assertEquals 0 <span class="nv" style="color: teal;">$?</span></span>
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<td class="diff-line-num old_line" data-linenumber="164" 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">
164
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<td class="diff-line-num new_line" data-linenumber="168" 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">
168
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="shell"></span>
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<td class="diff-line-num old old_line" data-linenumber="165" 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">
165
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> depth base <span class="nt" style="color: navy;">-c</span> 0 <span class="nb" style="color: #0086b3;">test</span>/issue225.bam <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: teal;">$outdir</span>/depth_base_225_0.txt 2>/dev/null</span>
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<td class="diff-line-num new old_line" data-linenumber="166" style="width: 35px; color: rgba(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="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> <span class="nv" style="color: teal;"><span class="idiff left">$opts</span></span><span class="idiff right"> </span>depth base <span class="nt" style="color: navy;">-c</span> 0 <span class="nb" style="color: #0086b3;">test</span>/issue225.bam <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: teal;">$outdir</span>/depth_base_225_0.txt 2>/dev/null</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
166
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<td class="diff-line-num new_line" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
170
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="shell"> diff <span class="nt" style="color: navy;">-q</span> <span class="nv" style="color: teal;">$outdir</span>/depth_base_225_0.txt <span class="nb" style="color: #0086b3;">test</span>/issue225.z.out</span>
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167
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171
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="shell"> assertEquals 0 <span class="nv" style="color: teal;">$?</span></span>
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<td class="diff-line-num old_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
168
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172
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="shell"></span>
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<td class="diff-line-num old_line" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
169
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<td class="diff-line-num new_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
173
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># exercise BED codepath as well</span></span>
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170
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<td class="diff-line-num new_line old" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> depth base <span class="nt" style="color: navy;">-c</span> 1 <span class="nt" style="color: navy;">-L</span> chrM <span class="nb" style="color: #0086b3;">test</span>/issue225.bam <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: teal;">$outdir</span>/depth_base_225_1.txt 2>/dev/null</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> <span class="nv" style="color: teal;"><span class="idiff left">$opts</span></span><span class="idiff right"> </span>depth base <span class="nt" style="color: navy;">-c</span> 1 <span class="nt" style="color: navy;">-L</span> chrM <span class="nb" style="color: #0086b3;">test</span>/issue225.bam <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: teal;">$outdir</span>/depth_base_225_1.txt 2>/dev/null</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="171" 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">
171
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<td class="diff-line-num new_line" data-linenumber="175" 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">
175
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="shell"> diff <span class="nt" style="color: navy;">-q</span> <span class="nv" style="color: teal;">$outdir</span>/depth_base_225_1.txt <span class="nb" style="color: #0086b3;">test</span>/issue225.out</span>
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<td class="diff-line-num old_line" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
172
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<td class="diff-line-num new_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
176
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="shell"> assertEquals 0 <span class="nv" style="color: teal;">$?</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="173" 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">
173
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<td class="diff-line-num new_line" data-linenumber="177" 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">
177
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="shell"></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="174" 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">
174
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<td class="diff-line-num new_line old" data-linenumber="178" 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="LC174" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> depth base <span class="nt" style="color: navy;">-c</span> 0 <span class="nt" style="color: navy;">-L</span> chrM <span class="nb" style="color: #0086b3;">test</span>/issue225.bam <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: teal;">$outdir</span>/depth_base_225_0.txt 2>/dev/null</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="175" style="width: 35px; color: rgba(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="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="shell"> <span class="nv" style="color: teal;">$sambamba</span> <span class="nv" style="color: teal;"><span class="idiff left">$opts</span></span><span class="idiff right"> </span>depth base <span class="nt" style="color: navy;">-c</span> 0 <span class="nt" style="color: navy;">-L</span> chrM <span class="nb" style="color: #0086b3;">test</span>/issue225.bam <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: teal;">$outdir</span>/depth_base_225_0.txt 2>/dev/null</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
175
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<td class="diff-line-num new_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
179
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC179" class="line" lang="shell"> diff <span class="nt" style="color: navy;">-q</span> <span class="nv" style="color: teal;">$outdir</span>/depth_base_225_0.txt <span class="nb" style="color: #0086b3;">test</span>/issue225.z.out</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="176" 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">
176
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<td class="diff-line-num new_line" data-linenumber="180" 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">
180
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC180" class="line" lang="shell"> assertEquals 0 <span class="nv" style="color: teal;">$?</span></span>
</pre>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="177" 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">
177
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<td class="diff-line-num new_line" data-linenumber="181" 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">
181
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC181" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="178" 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">
178
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<td class="diff-line-num new_line" data-linenumber="182" 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">
182
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC182" class="line" lang="shell"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="179" 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">
179
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<td class="diff-line-num new_line" data-linenumber="183" 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">
183
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC183" class="line" lang="shell">testIssue331<span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="180" 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">
180
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<td class="diff-line-num new_line old" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC180" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> view <span class="nt" style="color: navy;">-H</span> <span class="nt" style="color: navy;">-f</span> json <span class="nb" style="color: #0086b3;">test</span>/issue_204.bam <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: teal;">$outdir</span>/issue_331_header.json</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
184
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC184" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> <span class="nv" style="color: teal;"><span class="idiff left">$opts</span></span><span class="idiff right"> </span> view <span class="nt" style="color: navy;">-H</span> <span class="nt" style="color: navy;">-f</span> json <span class="nb" style="color: #0086b3;">test</span>/issue_204.bam <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: teal;">$outdir</span>/issue_331_header.json</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="181" 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">
181
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<td class="diff-line-num new_line" data-linenumber="185" 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">
185
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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="LC185" class="line" lang="shell"> assertEquals 0 <span class="nv" style="color: teal;">$?</span></span>
</pre>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
182
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<td class="diff-line-num new_line" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
186
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC186" class="line" lang="shell"> diff <span class="nt" style="color: navy;">-q</span> <span class="nv" style="color: teal;">$outdir</span>/issue_331_header.json <span class="nb" style="color: #0086b3;">test</span>/regression/issue_331_header.json</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="183" 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">
183
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<td class="diff-line-num new_line" data-linenumber="187" 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">
187
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC187" class="line" lang="shell"> assertEquals 0 <span class="nv" style="color: teal;">$?</span></span>
</pre>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="184" 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">
184
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<td class="diff-line-num new_line" data-linenumber="188" 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">
188
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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="LC188" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="185" 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">
185
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<td class="diff-line-num new_line" data-linenumber="189" 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">
189
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC189" class="line" lang="shell"></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="186" style="width: 35px; color: rgba(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="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
190
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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="LC190" class="line" lang="shell">testIssue356<span class="o" style="font-weight: 600;">(){</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
191
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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="LC191" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># check for missing PM tag in @RG</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
192
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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="LC192" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> <span class="nv" style="color: teal;">$opts</span> view <span class="nt" style="color: navy;">-S</span> <span class="nb" style="color: #0086b3;">test</span>/issue_356.sam <span class="nt" style="color: navy;">-f</span> bam <span class="nt" style="color: navy;">-o</span> <span class="nv" style="color: teal;">$outdir</span>/issue_356.bam</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
193
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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="LC193" class="line" lang="shell"> <span class="nv" style="color: teal;">$sambamba</span> <span class="nv" style="color: teal;">$opts</span> view <span class="nv" style="color: teal;">$outdir</span>/issue_356.bam <span class="nt" style="color: navy;">-H</span>|grep <span class="nt" style="color: navy;">-q</span> <span class="s2" style="color: #d14;">"PM:HiSeq2500_HighOutput"</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
194
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC194" class="line" lang="shell"> assertEquals 0 <span class="nv" style="color: teal;">$?</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
195
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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="LC195" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
196
</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="LC196" class="line" lang="shell"></span>
</pre>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="186" 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">
186
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<td class="diff-line-num new_line" data-linenumber="197" 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">
197
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC197" class="line" lang="shell"><span class="nv" style="color: teal;">shunit2</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span>which shunit2<span class="sb" style="color: #d14;">`</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="187" 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">
187
</td>
<td class="diff-line-num new_line" data-linenumber="198" 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">
198
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC198" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-x</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$shunit2</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
</pre>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
188
</td>
<td class="diff-line-num new_line" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
199
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC199" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">.</span> <span class="nv" style="color: teal;">$shunit2</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="189" 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">
189
</td>
<td class="diff-line-num new_line" data-linenumber="200" 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">
200
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC200" class="line" lang="shell"><span class="k" style="font-weight: 600;">else</span></span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="190" 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">
190
</td>
<td class="diff-line-num new_line old" data-linenumber="201" 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="LC190" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">.</span> <span class="idiff left right">shunit2-2.0.3/src/shell</span>/shunit2</span>
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">.</span> <span class="idiff left right">contrib/shunit2-2.0.3</span>/shunit2</span>
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191
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span></pre>
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<li id="f3336b1428b648374b0d29c18036eee01ed71db1">
<a href="https://salsa.debian.org/med-team/sambamba/commit/22dc4a7940dc5de9eada1184d972cdcab89ba973#f3336b1428b648374b0d29c18036eee01ed71db1"><strong>utils/version_.d</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="d"><span class="k" style="font-weight: 600;">module</span> <span class="n" style="color: #333;">utils</span><span class="p">.</span><span class="n" style="color: #333;">version_</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="d"></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="d"><span class="k" style="font-weight: 600;">immutable</span> <span class="nb" style="color: #0086b3;">string</span> <span class="n" style="color: #333;">VERSION</span> <span class="p">=</span> <span class="s" style="color: #d14;">"0.6.8<span class="idiff left right">-pre2</span>"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="d"><span class="k" style="font-weight: 600;">immutable</span> <span class="nb" style="color: #0086b3;">string</span> <span class="n" style="color: #333;">VERSION</span> <span class="p">=</span> <span class="s" style="color: #d14;">"0.6.8"</span><span class="p">;</span></span>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="d"><span class="k" style="font-weight: 600;">immutable</span> <span class="nb" style="color: #0086b3;">string</span> <span class="n" style="color: #333;">HEADER_VERSION</span> <span class="p">=</span> <span class="s" style="color: #d14;">"1.0"</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// goes in header for reproducibility between sambamba versions</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="d"></span>
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="d"><span class="k" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">bio</span><span class="p">.</span><span class="n" style="color: #333;">sam</span><span class="p">.</span><span class="n" style="color: #333;">header</span><span class="p">;</span></span>
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