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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/lastz">Debian Med / lastz</a>
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<h4>
Commits:
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<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/lastz/-/commit/b9c644b196583be0432474565bd2e451067b3937">b9c644b1</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-15T16:43:41+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add autopkgtest
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<h4>8 changed files:</h4>
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<li class="file-stats">
<a href="#f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
debian/README.test
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#f3bee93ccf2234de0a5119f212ab89b438a04bfa">
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debian/lastz-examples.install
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<li class="file-stats">
<a href="#96242d687fa4ce549bb960278eb041346cd11a13">
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debian/lastz.docs
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<li class="file-stats">
<a href="#d3e8a2c637be7b8408bf077dcb7ee0e856d0a37d">
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debian/lastz.install
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<li class="file-stats">
<a href="#36d9f10c399cace22f9ea6e1cdd8d797af0bcf57">
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debian/tests/Makefile
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<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
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<h4>Changes:</h4>
<li id="f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
<a href="https://salsa.debian.org/med-team/lastz/-/commit/b9c644b196583be0432474565bd2e451067b3937#f6a99a1e522a0f5ca122fd9818a9d8536ea59942"><strong>debian/README.test</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,6 +3,7 @@ Notes on how this package can be tested.</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="php"></span>
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<td class="diff-line-num new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="php"><span class="nx">This</span> <span class="nx">package</span> <span class="nx">can</span> <span class="nx">be</span> <span class="nx">tested</span> <span class="nx">by</span> <span class="nx">running</span> <span class="nx">the</span> <span class="nx">provided</span> <span class="nx">test</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="php"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="php"> <span class="nx">sudo</span> <span class="nx">apt</span><span class="o" style="font-weight: 600;">-</span><span class="nx">get</span> <span class="nx">install</span> <span class="nx">lastz</span><span class="o" style="font-weight: 600;">-</span><span class="nx">examples</span></span>
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<td class="diff-line-num new_line" data-linenumber="7" 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="LC7" class="line" lang="php"> <span class="nx">sh</span> <span class="nx">run</span><span class="o" style="font-weight: 600;">-</span><span class="nx">unit</span><span class="o" style="font-weight: 600;">-</span><span class="nx">test</span></span>
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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="php"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="php"><span class="nx">in</span> <span class="nx">order</span> <span class="nx">to</span> <span class="nx">confirm</span> <span class="nx">its</span> <span class="nx">integrity</span><span class="o" style="font-weight: 600;">.</span></span></pre>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/lastz/-/commit/b9c644b196583be0432474565bd2e451067b3937#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="18" 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="18" 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">@@ -18,3 +18,14 @@ Description: pairwise aligning DNA sequences</td>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> BLASTZ’s command-line syntax. That is, it supports all of BLASTZ’s options</span>
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<td class="diff-line-num old_line" data-linenumber="19" 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="LC19" class="line" lang="plaintext"> but also has additional ones, and may produce slightly different alignment</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> results.</span>
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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"></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">Package: lastz-examples</span>
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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">
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">Depends: ${python3:Depends}, ${misc:Depends}</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">Description: pairwise aligning DNA sequences (examples and test scripts)</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> LASTZ is a drop-in replacement for BLASTZ, and is backward compatible with</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> BLASTZ’s command-line syntax. That is, it supports all of BLASTZ’s options</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> but also has additional ones, and may produce slightly different alignment</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> results.</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> This package contains example data and test scripts.</span></pre>
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<a href="https://salsa.debian.org/med-team/lastz/-/commit/b9c644b196583be0432474565bd2e451067b3937#f3bee93ccf2234de0a5119f212ab89b438a04bfa"><strong>debian/lastz-examples.install</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nx">test_data</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">doc</span><span class="o" style="font-weight: 600;">/</span><span class="nx">lastz</span><span class="o" style="font-weight: 600;">/</span><span class="nx">examples</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="php"><span class="nx">tools</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">doc</span><span class="o" style="font-weight: 600;">/</span><span class="nx">lastz</span><span class="o" style="font-weight: 600;">/</span><span class="nx">examples</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="php"><span class="nx">debian</span><span class="o" style="font-weight: 600;">/</span><span class="nx">tests</span><span class="o" style="font-weight: 600;">/</span><span class="nx">Makefile</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">doc</span><span class="o" style="font-weight: 600;">/</span><span class="nx">lastz</span><span class="o" style="font-weight: 600;">/</span><span class="nx">examples</span><span class="o" style="font-weight: 600;">/</span><span class="nx">test_data</span></span></pre>
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<a href="https://salsa.debian.org/med-team/lastz/-/commit/b9c644b196583be0432474565bd2e451067b3937#96242d687fa4ce549bb960278eb041346cd11a13"><strong>debian/lastz.docs</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">docs</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">debian/README.test</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">debian/tests/run-unit-test</span></pre>
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<a href="https://salsa.debian.org/med-team/lastz/-/commit/b9c644b196583be0432474565bd2e451067b3937#d3e8a2c637be7b8408bf077dcb7ee0e856d0a37d"><strong>debian/lastz.install</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nx">src</span><span class="o" style="font-weight: 600;">/</span><span class="nx">lastz</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="php"><span class="nx">src</span><span class="o" style="font-weight: 600;">/</span><span class="nx">lastz_D</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span></span></pre>
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<a href="https://salsa.debian.org/med-team/lastz/-/commit/b9c644b196583be0432474565bd2e451067b3937#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="24" 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">@@ -24,6 +24,6 @@ export DEB_CFLAGS_MAINT_APPEND = -Wno-stringop-truncation</td>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">override_dh_auto_test:</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"> $(MAKE) base_tests</span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext"> <span class="idiff left right">#</span>$(MAKE) test</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> $(MAKE) test</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"> $(MAKE) clean_test</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext">endif</span></pre>
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<a href="https://salsa.debian.org/med-team/lastz/-/commit/b9c644b196583be0432474565bd2e451067b3937#36d9f10c399cace22f9ea6e1cdd8d797af0bcf57"><strong>debian/tests/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;">#---------</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;"># testing</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;"># Small tests to give some comfort level that the program has built properly,</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;"># or that changes you've made to the source code haven't broken it. The</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;"># results of lav_compare should be of this form:</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;"># SUCCESS: ../test_data/xxx and ../test_results/yyy are equivalent</span></span>
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8
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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;"># Note that a simple diff could be used in most cases, except that there will</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;"># be some mismatches due to version number differences. For the overweight</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;"># seed test, diff is useless since the files being compared will have seed hits</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;"># in different orders.</span></span>
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<pre style="margin: 0;">+<span id="LC13" 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;"># The tests:</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;"># test Same as base_test_default, but success is silent</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;"># (this is included for backward compatibility)</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># base_test_hits Seed hits only</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;"># base_test_hsp HSP alignments only</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;"># base_test_adaptive_k HSP alignments only, adaptive-K</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># base_test_default Default alignment (gapped without chaining)</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># base_test_axt AXT output format</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># base_test_chained chained HSPs</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># base_test_extended gapped alignments</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># base_test_interpolated interpolated alignments</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># base_test_segments reading and writing anchor segments</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># base_test_stdin2 sequence2 comes from stdin</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># base_test_2bit1 sequence1 comes from .2bit file</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># base_test_2bit2 sequence2 comes from .2bit file</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># base_test_float floating point scoring</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># base_test_seeded non-standard seed pattern</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># base_test_hw_seeded half weight seed pattern</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># base_test_ow_seeded overweight seed pattern</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># base_test_masking dynamic masking</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># base_test_anchors external anchors</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;"># base_test_anchors_multi external anchors with multi-sequence file</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># base_test_subrange sequence subranges</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># base_test_mask sequence masking</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># base_test_coi contigs-of-interest file</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># base_test_multi multi-sequence file</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># base_test_multi_subrange multi-sequence file with subranges</span></span>
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<pre style="margin: 0;">+<span id="LC41" 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="LC42" class="line" lang="make"></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="make"><span class="nv" style="color: #008080;">lavCompare</span> <span class="o" style="font-weight: 600;">=</span> ../tools/lav_compare.py</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="make"><span class="nv" style="color: #008080;">gfaCompare</span> <span class="o" style="font-weight: 600;">=</span> ../tools/gfa_compare.py</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="make"><span class="nv" style="color: #008080;">axtCompare</span> <span class="o" style="font-weight: 600;">=</span> ../tools/axt_compare.py</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="make"><span class="nv" style="color: #008080;">mafSort</span> <span class="o" style="font-weight: 600;">=</span> ../tools/maf_sort.py</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="make"></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="make"><span class="nl">clean_test</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">clean_tests</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="make"></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="make"><span class="nl">clean_tests</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> ../test_results/base_test<span class="k" style="font-weight: 600;">*</span>.<span class="k" style="font-weight: 600;">*</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="make"></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="make"><span class="nl">test</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> ../test_results/base_test.default.lav</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="make"> <span class="p">@</span>./lastz <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="make"> ../test_data/pseudocat.fa <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="make"> ../test_data/pseudopig.fa <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="make"> | <span class="nb" style="color: #0086b3;">sed</span> <span class="s2" style="color: #d14;">"s/</span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;">lastz</span><span class="se" style="color: #d14;">\.</span><span class="s2" style="color: #d14;">[^ ]* //g"</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="make"> <span class="o" style="font-weight: 600;">></span> ../test_results/base_test.default.lav</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="make"> <span class="p">@</span>diff <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="make"> ../test_data/base_test.default.lav <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="make"> ../test_results/base_test.default.lav</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="make"><span class="nl">base_tests</span><span class="o" style="font-weight: 600;">:</span> \</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_hits </span>\</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_hsp </span>\</span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_adaptive_k </span>\</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_default </span>\</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_axt </span>\</span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_chained </span>\</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_extended </span>\</span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_interpolated </span>\</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_segments </span>\</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_stdin2 </span>\</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_2bit1 </span>\</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_2bit2 </span>\</span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_float </span>\</span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_seeded </span>\</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_hw_seeded </span>\</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_ow_seeded </span>\</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_masking </span>\</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_anchors </span>\</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_anchors_multi </span>\</span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_subrange </span>\</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_mask </span>\</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_coi </span>\</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_multi </span>\</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_multi_subrange</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="make"></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="make"><span class="nl">base_tests_non_float</span><span class="o" style="font-weight: 600;">:</span> \</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_hits </span>\</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_hsp </span>\</span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_adaptive_k </span>\</span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_default </span>\</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_axt </span>\</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_chained </span>\</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_extended </span>\</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_interpolated </span>\</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_segments </span>\</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_stdin2 </span>\</span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_2bit1 </span>\</span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_2bit2 </span>\</span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_seeded </span>\</span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_hw_seeded </span>\</span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_ow_seeded </span>\</span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_masking </span>\</span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_anchors </span>\</span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_anchors_multi </span>\</span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_subrange </span>\</span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_mask </span>\</span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_coi </span>\</span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_multi </span>\</span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_multi_subrange</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="make"></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="make"><span class="nl">base_tests_no_stdin2</span><span class="o" style="font-weight: 600;">:</span> \</span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_hits </span>\</span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_hsp </span>\</span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_adaptive_k </span>\</span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_default </span>\</span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_axt </span>\</span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_chained </span>\</span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_extended </span>\</span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_interpolated </span>\</span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_segments </span>\</span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_2bit1 </span>\</span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_2bit2 </span>\</span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_float </span>\</span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_seeded </span>\</span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_hw_seeded </span>\</span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_ow_seeded </span>\</span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_masking </span>\</span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_anchors </span>\</span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_anchors_multi </span>\</span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_subrange </span>\</span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_mask </span>\</span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_coi </span>\</span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_multi </span>\</span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="make"><span class="nf" style="color: #900; font-weight: 600;"> base_test_multi_subrange</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="make"></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="make"><span class="nl">base_test_hits</span><span class="o" style="font-weight: 600;">:</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> ../test_results/base_test.hits.lav</span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="make"> <span class="p">@</span>/usr/bin/lastz <span class="se" style="color: #d14;">\</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="make"> ../test_data/pseudocat.fa <span class="se" style="color: #d14;">\</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="make"> ../test_data/pseudopig.fa <span class="se" style="color: #d14;">\</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="make"> <span class="nv" style="color: #008080;">W</span><span class="o" style="font-weight: 600;">=</span>8 <span class="nv" style="color: #008080;">T</span><span class="o" style="font-weight: 600;">=</span>0 <span class="nt" style="color: #000080;">--plus</span> <span class="nt" style="color: #000080;">--nogfextend</span> <span class="nt" style="color: #000080;">--nogapped</span> <span class="se" style="color: #d14;">\</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="make"> <span class="o" style="font-weight: 600;">></span> ../test_results/base_test.hits.lav</span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="make"> <span class="p">@</span><span class="nv" style="color: #008080;">${lavCompare}</span> <span class="se" style="color: #d14;">\</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="make"> ../test_data/base_test.hits.lav <span class="se" style="color: #d14;">\</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="make"> ../test_results/base_test.hits.lav</span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="make"><span class="nl">base_test_hsp</span><span class="o" style="font-weight: 600;">:</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> ../test_results/base_test.hsp.lav</span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="make"> <span class="p">@</span>/usr/bin/lastz <span class="se" style="color: #d14;">\</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="make"> ../test_data/pseudocat.fa <span class="se" style="color: #d14;">\</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="make"> ../test_data/pseudopig.fa <span class="se" style="color: #d14;">\</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="make"> <span class="nv" style="color: #008080;">C</span><span class="o" style="font-weight: 600;">=</span>3 <span class="nv" style="color: #008080;">W</span><span class="o" style="font-weight: 600;">=</span>8 <span class="nv" style="color: #008080;">T</span><span class="o" style="font-weight: 600;">=</span>0 <span class="se" style="color: #d14;">\</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="make"> <span class="o" style="font-weight: 600;">></span> ../test_results/base_test.hsp.lav</span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="make"> <span class="p">@</span><span class="nv" style="color: #008080;">${lavCompare}</span> <span class="se" style="color: #d14;">\</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="make"> ../test_data/base_test.hsp.lav <span class="se" style="color: #d14;">\</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="make"> ../test_results/base_test.hsp.lav</span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="make"></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="make"><span class="nl">base_test_adaptive_k</span><span class="o" style="font-weight: 600;">:</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> ../test_results/base_test.adaptive_k.gfa</span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="make"> <span class="p">@</span>/usr/bin/lastz <span class="se" style="color: #d14;">\</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="make"> ../test_data/aglobin.2bit/human <span class="se" style="color: #d14;">\</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="make"> ../test_data/aglobin.2bit/cow <span class="se" style="color: #d14;">\</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="make"> <span class="nv" style="color: #008080;">C</span><span class="o" style="font-weight: 600;">=</span>3 <span class="nv" style="color: #008080;">W</span><span class="o" style="font-weight: 600;">=</span>8 <span class="nv" style="color: #008080;">T</span><span class="o" style="font-weight: 600;">=</span>0 <span class="nt" style="color: #000080;">--noentropy</span> <span class="nv" style="color: #008080;">K</span><span class="o" style="font-weight: 600;">=</span>top50% <span class="nt" style="color: #000080;">--gfa</span> <span class="se" style="color: #d14;">\</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="make"> | <span class="nb" style="color: #0086b3;">grep</span> <span class="s2" style="color: #d14;">"^a"</span> | <span class="nb" style="color: #0086b3;">sort</span> <span class="nt" style="color: #000080;">-rn</span> <span class="nt" style="color: #000080;">-k</span> 4 <span class="se" style="color: #d14;">\</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="make"> <span class="o" style="font-weight: 600;">></span> ../test_results/base_test.adaptive_k.gfa</span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="make"> <span class="p">@</span><span class="nv" style="color: #008080;">${gfaCompare}</span> <span class="se" style="color: #d14;">\</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="make"> ../test_data/base_test.adaptive_k.gfa <span class="se" style="color: #d14;">\</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="make"> ../test_results/base_test.adaptive_k.gfa</span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="make"></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="make"><span class="nl">base_test_default</span><span class="o" style="font-weight: 600;">:</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> ../test_results/base_test.default.lav</span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="make"> <span class="p">@</span>/usr/bin/lastz <span class="se" style="color: #d14;">\</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="make"> ../test_data/pseudocat.fa <span class="se" style="color: #d14;">\</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="make"> ../test_data/pseudopig.fa <span class="se" style="color: #d14;">\</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="make"> | <span class="nb" style="color: #0086b3;">sed</span> <span class="s2" style="color: #d14;">"s/</span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;">lastz</span><span class="se" style="color: #d14;">\.</span><span class="s2" style="color: #d14;">[^ ]* //g"</span> <span class="se" style="color: #d14;">\</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="make"> <span class="o" style="font-weight: 600;">></span> ../test_results/base_test.default.lav</span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="make"> <span class="p">@</span><span class="nv" style="color: #008080;">${lavCompare}</span> <span class="se" style="color: #d14;">\</span></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="make"> ../test_data/base_test.default.lav <span class="se" style="color: #d14;">\</span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="make"> ../test_results/base_test.default.lav</span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="make"></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="make"><span class="nl">base_test_axt</span><span class="o" style="font-weight: 600;">:</span></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> ../test_results/base_test.default.axt</span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="make"> <span class="p">@</span>/usr/bin/lastz <span class="se" style="color: #d14;">\</span></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="make"> ../test_data/pseudocat.fa <span class="se" style="color: #d14;">\</span></span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="make"> ../test_data/pseudopig.fa <span class="se" style="color: #d14;">\</span></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="make"> <span class="nt" style="color: #000080;">--format</span><span class="o" style="font-weight: 600;">=</span>axt <span class="se" style="color: #d14;">\</span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="make"> <span class="o" style="font-weight: 600;">></span> ../test_results/base_test.default.axt</span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="make"> <span class="p">@</span><span class="nv" style="color: #008080;">${axtCompare}</span> <span class="se" style="color: #d14;">\</span></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="make"> ../test_data/base_test.default.axt <span class="se" style="color: #d14;">\</span></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="make"> ../test_results/base_test.default.axt</span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="make"></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="make"><span class="nl">base_test_chained</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> ../test_results/base_test.chained.lav</span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="make"> <span class="p">@</span>/usr/bin/lastz <span class="se" style="color: #d14;">\</span></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="make"> ../test_data/pseudocat.fa <span class="se" style="color: #d14;">\</span></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="make"> ../test_data/pseudopig.fa <span class="se" style="color: #d14;">\</span></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="make"> <span class="nv" style="color: #008080;">C</span><span class="o" style="font-weight: 600;">=</span>1 <span class="nv" style="color: #008080;">W</span><span class="o" style="font-weight: 600;">=</span>8 <span class="nv" style="color: #008080;">T</span><span class="o" style="font-weight: 600;">=</span>0 <span class="se" style="color: #d14;">\</span></span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="make"> <span class="o" style="font-weight: 600;">></span> ../test_results/base_test.chained.lav</span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="make"> <span class="p">@</span><span class="nv" style="color: #008080;">${lavCompare}</span> <span class="se" style="color: #d14;">\</span></span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="make"> ../test_data/base_test.chained.lav <span class="se" style="color: #d14;">\</span></span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="make"> ../test_results/base_test.chained.lav</span>
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206
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="make"><span class="nl">base_test_extended</span><span class="o" 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="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> ../test_results/base_test.extended.lav</span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="make"> <span class="p">@</span>/usr/bin/lastz <span class="se" style="color: #d14;">\</span></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="make"> ../test_data/pseudocat.fa <span class="se" style="color: #d14;">\</span></span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="make"> ../test_data/pseudopig.fa <span class="se" style="color: #d14;">\</span></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="make"> <span class="nv" style="color: #008080;">C</span><span class="o" style="font-weight: 600;">=</span>2 <span class="nv" style="color: #008080;">W</span><span class="o" style="font-weight: 600;">=</span>8 <span class="nv" style="color: #008080;">T</span><span class="o" style="font-weight: 600;">=</span>0 <span class="se" style="color: #d14;">\</span></span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="make"> <span class="o" style="font-weight: 600;">></span> ../test_results/base_test.extended.lav</span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="make"> <span class="p">@</span><span class="nv" style="color: #008080;">${lavCompare}</span> <span class="se" style="color: #d14;">\</span></span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="make"> ../test_data/base_test.extended.lav <span class="se" style="color: #d14;">\</span></span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="make"> ../test_results/base_test.extended.lav</span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="make"></span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="make"><span class="nl">base_test_interpolated</span><span class="o" style="font-weight: 600;">:</span></span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> ../test_results/base_test.interpolated.lav</span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="make"> <span class="p">@</span>/usr/bin/lastz <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="make"> ../test_data/pseudocat.fa <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="make"> ../test_data/pseudopig.fa <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="make"> <span class="nv" style="color: #008080;">C</span><span class="o" style="font-weight: 600;">=</span>2 <span class="nv" style="color: #008080;">W</span><span class="o" style="font-weight: 600;">=</span>8 <span class="nv" style="color: #008080;">T</span><span class="o" style="font-weight: 600;">=</span>0 <span class="nv" style="color: #008080;">H</span><span class="o" style="font-weight: 600;">=</span>2200 <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="make"> <span class="o" style="font-weight: 600;">></span> ../test_results/base_test.interpolated.lav</span>
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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="make"> <span class="p">@</span><span class="nv" style="color: #008080;">${lavCompare}</span> <span class="se" style="color: #d14;">\</span></span>
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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="make"> ../test_data/base_test.interpolated.lav <span class="se" style="color: #d14;">\</span></span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="make"> ../test_results/base_test.interpolated.lav</span>
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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="make"></span>
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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="make"><span class="nl">base_test_segments</span><span class="o" style="font-weight: 600;">:</span></span>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> ../test_results/base_test.segments.hsps</span>
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231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> ../test_results/base_test.segments.lav</span>
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232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="make"> <span class="p">@</span>/usr/bin/lastz <span class="se" style="color: #d14;">\</span></span>
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233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="make"> ../test_data/pseudocat.fa <span class="se" style="color: #d14;">\</span></span>
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234
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="make"> ../test_data/pseudopig.fa <span class="se" style="color: #d14;">\</span></span>
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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="make"> <span class="nt" style="color: #000080;">--nogapped</span> <span class="nt" style="color: #000080;">--format</span><span class="o" style="font-weight: 600;">=</span>segments <span class="se" style="color: #d14;">\</span></span>
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236
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="make"> <span class="o" style="font-weight: 600;">></span> ../test_results/base_test.segments.hsps</span>
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237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="make"> <span class="p">@</span>/usr/bin/lastz <span class="se" style="color: #d14;">\</span></span>
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238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="make"> ../test_data/pseudocat.fa <span class="se" style="color: #d14;">\</span></span>
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239
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="make"> ../test_data/pseudopig.fa <span class="se" style="color: #d14;">\</span></span>
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240
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="make"> <span class="nt" style="color: #000080;">--segments</span><span class="o" style="font-weight: 600;">=</span>../test_results/base_test.segments.hsps <span class="se" style="color: #d14;">\</span></span>
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241
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="make"> | <span class="nb" style="color: #0086b3;">sed</span> <span class="s2" style="color: #d14;">"s/</span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;">lastz</span><span class="se" style="color: #d14;">\.</span><span class="s2" style="color: #d14;">[^ ]* //g"</span> <span class="se" style="color: #d14;">\</span></span>
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242
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="make"> <span class="o" style="font-weight: 600;">></span> ../test_results/base_test.segments.lav</span>
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243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="make"> <span class="p">@</span><span class="nv" style="color: #008080;">${lavCompare}</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="make"> ../test_data/base_test.default.lav <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="make"> ../test_results/base_test.segments.lav</span>
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246
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247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="make"><span class="nl">base_test_stdin2</span><span class="o" style="font-weight: 600;">:</span></span>
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248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> ../test_results/base_test.stdin2.lav</span>
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249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">cat</span> ../test_data/pseudopig.fa <span class="se" style="color: #d14;">\</span></span>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="make"> | /usr/bin/lastz <span class="se" style="color: #d14;">\</span></span>
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251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="make"> ../test_data/pseudocat.fa <span class="se" style="color: #d14;">\</span></span>
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252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="make"> <span class="nv" style="color: #008080;">C</span><span class="o" style="font-weight: 600;">=</span>3 <span class="nv" style="color: #008080;">W</span><span class="o" style="font-weight: 600;">=</span>8 <span class="nv" style="color: #008080;">T</span><span class="o" style="font-weight: 600;">=</span>0 <span class="se" style="color: #d14;">\</span></span>
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253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="make"> | <span class="nb" style="color: #0086b3;">sed</span> <span class="s2" style="color: #d14;">"s/(stdin)/..</span><span class="se" style="color: #d14;">\/</span><span class="s2" style="color: #d14;">test_data</span><span class="se" style="color: #d14;">\/</span><span class="s2" style="color: #d14;">pseudopig.fa/g"</span> <span class="se" style="color: #d14;">\</span></span>
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="make"> <span class="o" style="font-weight: 600;">></span> ../test_results/base_test.stdin2.lav</span>
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255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="make"> <span class="p">@</span><span class="nv" style="color: #008080;">${lavCompare}</span> <span class="se" style="color: #d14;">\</span></span>
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256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="make"> ../test_data/base_test.hsp.lav <span class="se" style="color: #d14;">\</span></span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="make"> ../test_results/base_test.stdin2.lav</span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="make"></span>
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259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="make"><span class="nl">base_test_nib1</span><span class="o" style="font-weight: 600;">:</span></span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> ../test_results/base_test.nib1.lav</span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="make"> <span class="p">@</span>/usr/bin/lastz <span class="se" style="color: #d14;">\</span></span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="make"> ../test_data/pseudopig2.nib <span class="se" style="color: #d14;">\</span></span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="make"> ../test_data/pseudocat.fa <span class="se" style="color: #d14;">\</span></span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="make"> <span class="nv" style="color: #008080;">C</span><span class="o" style="font-weight: 600;">=</span>2 <span class="nv" style="color: #008080;">W</span><span class="o" style="font-weight: 600;">=</span>8 <span class="nv" style="color: #008080;">T</span><span class="o" style="font-weight: 600;">=</span>0 <span class="se" style="color: #d14;">\</span></span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="make"> | <span class="nb" style="color: #0086b3;">sed</span> <span class="s2" style="color: #d14;">"s/</span><span class="se" style="color: #d14;">\.\.</span><span class="s2" style="color: #d14;">.*</span><span class="se" style="color: #d14;">\.</span><span class="s2" style="color: #d14;">nib:.*</span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;">/> pig2</span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;">/g"</span> <span class="se" style="color: #d14;">\</span></span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="make"> | <span class="nb" style="color: #0086b3;">sed</span> <span class="s2" style="color: #d14;">"s/</span><span class="se" style="color: #d14;">\.</span><span class="s2" style="color: #d14;">nib/.fa/g"</span> <span class="se" style="color: #d14;">\</span></span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="make"> <span class="o" style="font-weight: 600;">></span> ../test_results/base_test.nib1.lav</span>
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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="make"> <span class="p">@</span><span class="nv" style="color: #008080;">${lavCompare}</span> <span class="se" style="color: #d14;">\</span></span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="make"> ../test_data/base_test.pig_cat.lav <span class="se" style="color: #d14;">\</span></span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="make"> ../test_results/base_test.nib1.lav</span>
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="make"></span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="make"><span class="nl">base_test_2bit1</span><span class="o" style="font-weight: 600;">:</span></span>
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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> ../test_results/base_test.2bit1.lav</span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="make"> <span class="p">@</span>/usr/bin/lastz <span class="se" style="color: #d14;">\</span></span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="make"> ../test_data/pseudopig.2bit/pig2 <span class="se" style="color: #d14;">\</span></span>
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="make"> ../test_data/pseudocat.fa <span class="se" style="color: #d14;">\</span></span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="make"> <span class="nv" style="color: #008080;">C</span><span class="o" style="font-weight: 600;">=</span>2 <span class="nv" style="color: #008080;">W</span><span class="o" style="font-weight: 600;">=</span>8 <span class="nv" style="color: #008080;">T</span><span class="o" style="font-weight: 600;">=</span>0 <span class="se" style="color: #d14;">\</span></span>
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278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="make"> | <span class="nb" style="color: #0086b3;">sed</span> <span class="s2" style="color: #d14;">"s/pig/> pig/g"</span> <span class="se" style="color: #d14;">\</span></span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="make"> | <span class="nb" style="color: #0086b3;">sed</span> <span class="s2" style="color: #d14;">"s/do> pig.2bit/dopig2.fa/g"</span> <span class="se" style="color: #d14;">\</span></span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="make"> | <span class="nb" style="color: #0086b3;">sed</span> <span class="s2" style="color: #d14;">"s/</span><span class="se" style="color: #d14;">\(</span><span class="s2" style="color: #d14;">dopig2.*</span><span class="se" style="color: #d14;">\)</span><span class="s2" style="color: #d14;"> 0 2/</span><span class="se" style="color: #d14;">\1</span><span class="s2" style="color: #d14;"> 0 1/g"</span> <span class="se" style="color: #d14;">\</span></span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="make"> <span class="o" style="font-weight: 600;">></span> ../test_results/base_test.2bit1.lav</span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="make"> <span class="p">@</span><span class="nv" style="color: #008080;">${lavCompare}</span> <span class="se" style="color: #d14;">\</span></span>
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="make"> ../test_data/base_test.pig_cat.lav <span class="se" style="color: #d14;">\</span></span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="make"> ../test_results/base_test.2bit1.lav</span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="make"></span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="make"><span class="nl">base_test_2bit2</span><span class="o" style="font-weight: 600;">:</span></span>
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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> ../test_results/base_test.2bit2.lav</span>
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288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="make"> <span class="p">@</span>/usr/bin/lastz <span class="se" style="color: #d14;">\</span></span>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="make"> ../test_data/pseudocat.fa <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="make"> ../test_data/pseudopig.2bit <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="make"> <span class="nv" style="color: #008080;">C</span><span class="o" style="font-weight: 600;">=</span>2 <span class="nv" style="color: #008080;">W</span><span class="o" style="font-weight: 600;">=</span>8 <span class="nv" style="color: #008080;">T</span><span class="o" style="font-weight: 600;">=</span>0 <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="make"> | <span class="nb" style="color: #0086b3;">sed</span> <span class="s2" style="color: #d14;">"s/pig/> pig/g"</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="make"> | <span class="nb" style="color: #0086b3;">sed</span> <span class="s2" style="color: #d14;">"s/do> pig.2bit/dopig.fa/g"</span> <span class="se" style="color: #d14;">\</span></span>
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294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="make"> <span class="o" style="font-weight: 600;">></span> ../test_results/base_test.2bit2.lav</span>
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="make"> <span class="p">@</span><span class="nv" style="color: #008080;">${lavCompare}</span> <span class="se" style="color: #d14;">\</span></span>
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="make"> ../test_data/base_test.extended.lav <span class="se" style="color: #d14;">\</span></span>
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297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="make"> ../test_results/base_test.2bit2.lav</span>
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298
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="make"><span class="nl">base_test_float</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> ../test_results/base_test.float.lav</span>
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301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="make"> <span class="p">@</span>/usr/bin/lastz_D <span class="se" style="color: #d14;">\</span></span>
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302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="make"> ../test_data/pseudocat.fa <span class="se" style="color: #d14;">\</span></span>
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303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="make"> ../test_data/pseudopig.fa <span class="se" style="color: #d14;">\</span></span>
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304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="make"> <span class="nv" style="color: #008080;">C</span><span class="o" style="font-weight: 600;">=</span>2 <span class="nv" style="color: #008080;">W</span><span class="o" style="font-weight: 600;">=</span>8 <span class="nv" style="color: #008080;">T</span><span class="o" style="font-weight: 600;">=</span>0 <span class="se" style="color: #d14;">\</span></span>
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305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="make"> <span class="o" style="font-weight: 600;">></span> ../test_results/base_test.float.lav</span>
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306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="make"> <span class="p">@</span><span class="nv" style="color: #008080;">${lavCompare}</span> <span class="se" style="color: #d14;">\</span></span>
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307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="make"> ../test_data/base_test.float.lav <span class="se" style="color: #d14;">\</span></span>
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308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="make"> ../test_results/base_test.float.lav</span>
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309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="make"></span>
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310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="make"><span class="nl">base_test_seeded</span><span class="o" style="font-weight: 600;">:</span></span>
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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> ../test_results/base_test.seeded.lav</span>
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312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="make"> <span class="p">@</span>/usr/bin/lastz <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="make"> ../test_data/pseudocat.fa <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="make"> ../test_data/pseudopig.fa <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="make"> <span class="nv" style="color: #008080;">C</span><span class="o" style="font-weight: 600;">=</span>3 <span class="nt" style="color: #000080;">--seed</span><span class="o" style="font-weight: 600;">=</span>111010011101 <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="make"> <span class="o" style="font-weight: 600;">></span> ../test_results/base_test.seeded.lav</span>
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="make"> <span class="p">@</span><span class="nv" style="color: #008080;">${lavCompare}</span> <span class="se" style="color: #d14;">\</span></span>
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318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="make"> ../test_data/base_test.seeded.lav <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="make"> ../test_results/base_test.seeded.lav</span>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="make"><span class="nl">base_test_hw_seeded</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> ../test_results/base_test.hwseeded.lav</span>
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323
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="make"> <span class="p">@</span>/usr/bin/lastz <span class="se" style="color: #d14;">\</span></span>
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324
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="make"> ../test_data/pseudocat.fa <span class="se" style="color: #d14;">\</span></span>
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325
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="make"> ../test_data/pseudopig.fa <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="make"> <span class="nv" style="color: #008080;">C</span><span class="o" style="font-weight: 600;">=</span>3 <span class="nt" style="color: #000080;">--seed</span><span class="o" style="font-weight: 600;">=</span>TTT0T0T0TTT00T0T <span class="se" style="color: #d14;">\</span></span>
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327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="make"> <span class="o" style="font-weight: 600;">></span> ../test_results/base_test.hwseeded.lav</span>
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328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="make"> <span class="p">@</span><span class="nv" style="color: #008080;">${lavCompare}</span> <span class="se" style="color: #d14;">\</span></span>
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329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="make"> ../test_data/base_test.hwseeded.lav <span class="se" style="color: #d14;">\</span></span>
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330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="make"> ../test_results/base_test.hwseeded.lav</span>
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331
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332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="make"><span class="nl">base_test_ow_seeded</span><span class="o" style="font-weight: 600;">:</span></span>
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333
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> ../test_results/base_test.owseeded.gfa</span>
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334
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="make"> <span class="p">@</span>/usr/bin/lastz <span class="se" style="color: #d14;">\</span></span>
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335
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="make"> ../test_data/pseudocat.fa <span class="se" style="color: #d14;">\</span></span>
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336
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="make"> ../test_data/pseudopig.fa <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="make"> <span class="nt" style="color: #000080;">--justhits</span> <span class="nt" style="color: #000080;">--seed</span><span class="o" style="font-weight: 600;">=</span>111010011101 <span class="nt" style="color: #000080;">--word</span><span class="o" style="font-weight: 600;">=</span>12 <span class="se" style="color: #d14;">\</span></span>
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338
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="make"> <span class="nt" style="color: #000080;">--gfa</span> <span class="se" style="color: #d14;">\</span></span>
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339
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="make"> <span class="o" style="font-weight: 600;">></span> ../test_results/base_test.owseeded.gfa</span>
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340
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="make"> <span class="p">@</span><span class="nv" style="color: #008080;">${gfaCompare}</span> <span class="nt" style="color: #000080;">--sort</span> <span class="se" style="color: #d14;">\</span></span>
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341
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="make"> ../test_data/base_test.owseeded.gfa <span class="se" style="color: #d14;">\</span></span>
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342
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="make"> ../test_results/base_test.owseeded.gfa</span>
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343
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="make"></span>
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344
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="make"><span class="nl">base_test_masking</span><span class="o" style="font-weight: 600;">:</span></span>
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345
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> ../test_results/base_test.masking.lav</span>
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346
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="make"> <span class="p">@</span>/usr/bin/lastz <span class="se" style="color: #d14;">\</span></span>
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347
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="make"> ../test_data/fake_apple.fa <span class="se" style="color: #d14;">\</span></span>
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348
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="make"> ../test_data/fake_orange_reads.fa <span class="se" style="color: #d14;">\</span></span>
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349
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="make"> <span class="nt" style="color: #000080;">--masking</span><span class="o" style="font-weight: 600;">=</span>3 <span class="se" style="color: #d14;">\</span></span>
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350
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="make"> <span class="o" style="font-weight: 600;">></span> ../test_results/base_test.masking.lav</span>
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351
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="make"> <span class="p">@</span><span class="nv" style="color: #008080;">${lavCompare}</span> <span class="se" style="color: #d14;">\</span></span>
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352
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="make"> ../test_data/base_test.masking.lav <span class="se" style="color: #d14;">\</span></span>
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353
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="make"> ../test_results/base_test.masking.lav</span>
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354
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="make"></span>
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355
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="make"><span class="nl">base_test_anchors</span><span class="o" style="font-weight: 600;">:</span></span>
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356
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> ../test_results/base_test.anchors.maf</span>
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357
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="make"> <span class="p">@</span>/usr/bin/lastz <span class="se" style="color: #d14;">\</span></span>
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358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="make"> ../test_data/aglobin.2bit/human <span class="se" style="color: #d14;">\</span></span>
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359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="make"> ../test_data/aglobin.2bit/cow <span class="se" style="color: #d14;">\</span></span>
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360
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="make"> <span class="nv" style="color: #008080;">C</span><span class="o" style="font-weight: 600;">=</span>0 <span class="nt" style="color: #000080;">--format</span><span class="o" style="font-weight: 600;">=</span>maf- <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="make"> <span class="nt" style="color: #000080;">--anchors</span><span class="o" style="font-weight: 600;">=</span>../test_data/base_test.anchors.anchors <span class="se" style="color: #d14;">\</span></span>
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362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="make"> <span class="o" style="font-weight: 600;">></span> ../test_results/base_test.anchors.maf</span>
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="make"> ../test_data/base_test.anchors.maf <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="make"> ../test_results/base_test.anchors.maf</span>
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366
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="make"><span class="nl">base_test_anchors_multi</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> ../test_results/base_test.anchors_multi.maf</span>
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369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="make"> <span class="p">@</span>/usr/bin/lastz <span class="se" style="color: #d14;">\</span></span>
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370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="make"> ../test_data/aglobin.2bit/human <span class="se" style="color: #d14;">\</span></span>
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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="make"> ../test_data/shorties.fa[subset<span class="o" style="font-weight: 600;">=</span>../test_data/shorties.names] <span class="se" style="color: #d14;">\</span></span>
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372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="make"> <span class="nv" style="color: #008080;">C</span><span class="o" style="font-weight: 600;">=</span>0 <span class="nt" style="color: #000080;">--format</span><span class="o" style="font-weight: 600;">=</span>maf- <span class="se" style="color: #d14;">\</span></span>
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373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="make"> <span class="nt" style="color: #000080;">--anchors</span><span class="o" style="font-weight: 600;">=</span>../test_data/base_test.anchors_multi.anchors <span class="se" style="color: #d14;">\</span></span>
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374
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="make"> <span class="o" style="font-weight: 600;">></span> ../test_results/base_test.anchors_multi.maf</span>
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375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="make"> <span class="p">@</span>diff <span class="se" style="color: #d14;">\</span></span>
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376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="make"> ../test_data/base_test.anchors_multi.maf <span class="se" style="color: #d14;">\</span></span>
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377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="make"> ../test_results/base_test.anchors_multi.maf</span>
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378
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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="make"><span class="nl">base_test_subrange</span><span class="o" style="font-weight: 600;">:</span></span>
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380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="make"> <span class="p">@</span>/usr/bin/lastz <span class="se" style="color: #d14;">\</span></span>
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381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="make"> ../test_data/aglobin.2bit/human[10000,60000] <span class="se" style="color: #d14;">\</span></span>
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382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="make"> ../test_data/aglobin.2bit/cow[15000#40000] <span class="se" style="color: #d14;">\</span></span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="make"> <span class="o" style="font-weight: 600;">></span> ../test_results/base_test.subrange.lav</span>
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384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="make"> <span class="p">@</span><span class="nv" style="color: #008080;">${lavCompare}</span> <span class="se" style="color: #d14;">\</span></span>
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385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="make"> ../test_data/base_test.subrange.lav <span class="se" style="color: #d14;">\</span></span>
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386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="make"> ../test_results/base_test.subrange.lav</span>
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387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="make"></span>
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388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="make"><span class="nl">base_test_mask</span><span class="o" style="font-weight: 600;">:</span></span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="make"> <span class="p">@</span>/usr/bin/lastz <span class="se" style="color: #d14;">\</span></span>
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390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="make"> ../test_data/pseudocat.fa <span class="se" style="color: #d14;">\</span></span>
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="make"> ../test_data/pseudopig.fa[nmask<span class="o" style="font-weight: 600;">=</span>../test_data/pseudopig.n.mask] <span class="se" style="color: #d14;">\</span></span>
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392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="make"> <span class="nt" style="color: #000080;">--ambiguous</span><span class="o" style="font-weight: 600;">=</span>n,60 <span class="se" style="color: #d14;">\</span></span>
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="make"> <span class="o" style="font-weight: 600;">></span> ../test_results/base_test.mask.lav</span>
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394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="make"> <span class="p">@</span><span class="nv" style="color: #008080;">${lavCompare}</span> <span class="se" style="color: #d14;">\</span></span>
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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="make"> ../test_data/base_test.mask.lav <span class="se" style="color: #d14;">\</span></span>
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396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="make"> ../test_results/base_test.mask.lav</span>
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397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="make"></span>
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398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="make"><span class="nl">base_test_coi</span><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="make"> <span class="p">@</span>/usr/bin/lastz <span class="se" style="color: #d14;">\</span></span>
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400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="make"> ../test_data/aglobin.2bit/human <span class="se" style="color: #d14;">\</span></span>
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401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="make"> ../test_data/shorties.fa[subset<span class="o" style="font-weight: 600;">=</span>../test_data/shorties.names] <span class="se" style="color: #d14;">\</span></span>
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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="make"> <span class="nv" style="color: #008080;">K</span><span class="o" style="font-weight: 600;">=</span>3000 <span class="nt" style="color: #000080;">--maf-</span> <span class="se" style="color: #d14;">\</span></span>
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403
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="make"> <span class="o" style="font-weight: 600;">></span> ../test_results/base_test.coi_fa.maf</span>
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404
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="make"> <span class="p">@</span>diff <span class="se" style="color: #d14;">\</span></span>
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405
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="make"> ../test_data/base_test.coi.maf <span class="se" style="color: #d14;">\</span></span>
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406
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="make"> ../test_results/base_test.coi_fa.maf</span>
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407
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="make"> <span class="p">@</span>/usr/bin/lastz <span class="se" style="color: #d14;">\</span></span>
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408
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="make"> ../test_data/aglobin.2bit/human <span class="se" style="color: #d14;">\</span></span>
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409
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="make"> ../test_data/shorties.2bit[subset<span class="o" style="font-weight: 600;">=</span>../test_data/shorties.names] <span class="se" style="color: #d14;">\</span></span>
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410
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="make"> <span class="nv" style="color: #008080;">K</span><span class="o" style="font-weight: 600;">=</span>3000 <span class="nt" style="color: #000080;">--maf-</span> <span class="se" style="color: #d14;">\</span></span>
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411
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="make"> <span class="o" style="font-weight: 600;">></span> ../test_results/base_test.coi_2bit.maf</span>
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412
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="make"> <span class="p">@</span>diff <span class="se" style="color: #d14;">\</span></span>
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413
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="make"> ../test_data/base_test.coi.maf <span class="se" style="color: #d14;">\</span></span>
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414
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="make"> ../test_results/base_test.coi_2bit.maf</span>
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415
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="make"></span>
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416
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="make"><span class="nl">base_test_multi</span><span class="o" style="font-weight: 600;">:</span></span>
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417
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="make"> <span class="p">@</span>/usr/bin/lastz <span class="se" style="color: #d14;">\</span></span>
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418
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="make"> ../test_data/aglobin.2bit/human <span class="se" style="color: #d14;">\</span></span>
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419
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="make"> ../test_data/shorties.2bit[multi,@../test_data/shorties.names] <span class="se" style="color: #d14;">\</span></span>
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420
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="make"> <span class="nv" style="color: #008080;">K</span><span class="o" style="font-weight: 600;">=</span>3000 <span class="nt" style="color: #000080;">--maf-</span> <span class="se" style="color: #d14;">\</span></span>
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421
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="make"> | <span class="nv" style="color: #008080;">${mafSort}</span> <span class="nt" style="color: #000080;">--key</span><span class="o" style="font-weight: 600;">=</span>pos1 <span class="se" style="color: #d14;">\</span></span>
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422
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="make"> <span class="o" style="font-weight: 600;">></span> ../test_results/base_test.multi.maf</span>
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423
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="make"> <span class="p">@</span>diff <span class="se" style="color: #d14;">\</span></span>
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424
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="make"> ../test_data/base_test.multi.maf <span class="se" style="color: #d14;">\</span></span>
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425
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="make"> ../test_results/base_test.multi.maf</span>
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426
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427
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="make"><span class="nl">base_test_multi_subrange</span><span class="o" style="font-weight: 600;">:</span></span>
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428
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="make"> <span class="p">@</span>/usr/bin/lastz <span class="se" style="color: #d14;">\</span></span>
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429
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="make"> ../test_data/aglobin.2bit/human <span class="se" style="color: #d14;">\</span></span>
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430
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="make"> ../test_data/shorties.2bit[multi,51..200] <span class="se" style="color: #d14;">\</span></span>
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431
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="make"> <span class="nv" style="color: #008080;">K</span><span class="o" style="font-weight: 600;">=</span>3000 <span class="nt" style="color: #000080;">--maf-</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="make"> <span class="o" style="font-weight: 600;">></span> ../test_results/base_test.multi_subrange.maf</span>
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="make"> <span class="p">@</span>diff <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="make"> ../test_data/base_test.multi_subrange.maf <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="make"> ../test_results/base_test.multi_subrange.maf</span>
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="make"></span></pre>
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<li id="8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<a href="https://salsa.debian.org/med-team/lastz/-/commit/b9c644b196583be0432474565bd2e451067b3937#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash</span></span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span></span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="shell"></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="shell"><span class="nv" style="color: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span><span class="c" style="color: #998; font-style: italic;"><span class="idiff left right">#PACKAGENAME#</span></span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="nv" style="color: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span><span class="idiff left right">lastz</span></span>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="shell"></span>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">LC_ALL</span><span class="o" style="font-weight: 600;">=</span>C.UTF-8</span>
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7
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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8
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="si" style="color: #d14;">)</span></span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># Double quote below to expand the temporary directory variable now versus</span></span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># later is on purpose.</span></span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># shellcheck disable=SC2064</span></span>
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12
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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13
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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14
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="shell"></span>
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15
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/examples/<span class="k" style="font-weight: 600;">*</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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16
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="shell"></span>
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17
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<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="shell"><span class="nb" style="color: #0086b3;">gunzip</span> <span class="nt" style="color: #000080;">-r</span> <span class="k" style="font-weight: 600;">*</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="nb" style="color: #0086b3;">mkdir </span>test_results</span>
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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="nb" style="color: #0086b3;">chmod</span> +x tools/<span class="k" style="font-weight: 600;">*</span></span>
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18
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="shell"></span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#do_stuff_to_test_package#</span></span></pre>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>test_data</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell">make base_tests</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell">make <span class="nb" style="color: #0086b3;">test</span></span></pre>
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