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<h3>
Shayan Doust pushed to branch master
at <a href="https://salsa.debian.org/med-team/mmseqs2">Debian Med / mmseqs2</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/mmseqs2/commit/968f4d6ec81844e7d448281bfed3a52b3b01fba1">968f4d6e</a></strong>
<div>
<span>by Shayan Doust</span>
<i>at 2019-07-20T17:09:47Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix test_bestalphabet binary. Now works.
This is used within autopkgtest
</pre>
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<h4>2 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#5d4bc5bec9cccce49eb00b14a49d6fa0feedbf70">
debian/patches/fix_tests.patch
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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="5d4bc5bec9cccce49eb00b14a49d6fa0feedbf70">
<a href="https://salsa.debian.org/med-team/mmseqs2/commit/968f4d6ec81844e7d448281bfed3a52b3b01fba1#5d4bc5bec9cccce49eb00b14a49d6fa0feedbf70"><strong>debian/patches/fix_tests.patch</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6,8 +6,8 @@ Last-Update: 2019-07-20</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"><span class="gh" style="color: #999;">Index: mmseqs2/src/test/TestScoreMatrixSerialization.cpp</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- mmseqs2.orig/src/test/TestScoreMatrixSerialization.cpp 2019-07-20 1<span class="idiff left right">6:32:20.107321242</span> +0100</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ mmseqs2/src/test/TestScoreMatrixSerialization.cpp 2019-07-20 1<span class="idiff left right">6:32:58.363643912</span> +0100</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- mmseqs2.orig/src/test/TestScoreMatrixSerialization.cpp 2019-07-20 1<span class="idiff left right">7:51:23.891331720</span> +0100</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ mmseqs2/src/test/TestScoreMatrixSerialization.cpp 2019-07-20 1<span class="idiff left right">7:51:23.879331619</span> +0100</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -18,10 +18,12 @@</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="diff"> ScoreMatrix* unserialized = ScoreMatrix::unserialize(serialized, subMat.alphabetSize, 3);</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="diff"> </span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -25,3 +25,27 @@ Index: mmseqs2/src/test/TestScoreMatrixSerialization.cpp</td>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ </span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="diff"> return EXIT_SUCCESS;</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gh" style="color: #999;">Index: mmseqs2/src/test/TestBestAlphabet.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- mmseqs2.orig/src/test/TestBestAlphabet.cpp 2019-07-20 08:12:45.250499276 +0100</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ mmseqs2/src/test/TestBestAlphabet.cpp 2019-07-20 17:52:58.384128682 +0100</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -58,7 +58,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> ///////// | ////////////////</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> ///////// Choose substitution matrix here V ! ////////////////</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> //SubstitutionMatrix subMat("/Users/soeding/Projects/MMseqs2/MMseqs2/data/blosum100.out", 2.0, -0.0f);</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- SubstitutionMatrix subMat("/Users/soeding/Projects/MMseqs2/MMseqs2/data/PAM70.out", 2.0, -0.0f);</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ SubstitutionMatrix subMat("../example-data/PAM70.out", 2.0, -0.0f);</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> const size_t numAAs = subMat.alphabetSize-1; // size of original alphabet</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> const size_t numKmers = pow(numAAs,kmerSize);</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -72,8 +72,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> //////////////////////////////////////////////////////////////////////////////////////////////</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> // Compute probabilities for all 20^k k-mers in a sequence database "seqDB"</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- std::string dbPath = "seqDB";</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- std::string dbIndexPath = "seqDB.index";</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ std::string dbPath = "../example-data/DB";</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ std::string dbIndexPath = "../example-data/DB.index";</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> DBReader<unsigned int> seqDb(dbPath.c_str(), dbIndexPath.c_str(), 1, DBReader<unsigned int>::USE_DATA|DBReader<unsigned int>::USE_INDEX);</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> seqDb.open(DBReader<unsigned int>::NOSORT);</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> </span></pre>
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<li id="8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<a href="https://salsa.debian.org/med-team/mmseqs2/commit/968f4d6ec81844e7d448281bfed3a52b3b01fba1#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -9,6 +9,14 @@ if [ "${AUTOPKGTEST_TMP}" = "" ] ; then</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-r</span> /usr/lib/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/test <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-r</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/example-data <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Build some data for the test binaries as prerequisites</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</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>/example-data</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;">gunzip</span> <span class="k" style="font-weight: 600;">*</span>.gz</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"></span>
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<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell">mmseqs createdb DB.fasta DB</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell">mmseqs createindex DB tmp</span>
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12
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="shell"></span>
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13
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21
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<pre style="margin: 0;"> <span id="LC21" 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>/test</span>
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14
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="shell"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="57" 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="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -57,3 +65,5 @@ echo "Invoking test_util"</td>
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57
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65
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="shell">./test_util</span>
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58
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66
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Invoking test_scorematrixserialization"</span></span>
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59
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67
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="shell">./test_scorematrixserialization</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Invoking test_bestalphabet"</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="shell">./test_bestalphabet</span></pre>
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