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<h3>
Michael R. Crusoe pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/last-align">Debian Med / last-align</a>
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<h4>
Commits:
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<ul>
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<strong><a href="https://salsa.debian.org/med-team/last-align/commit/1114371359a004321568097e7d1c60eeb26e63c2">11143713</a></strong>
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<span>by Michael R. Crusoe</span>
<i>at 2020-01-24T15:47:34+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1047</pre>
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<h4>4 changed files:</h4>
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<li class="file-stats">
<a href="#57bf262130f956caf76c405086f0815caf4e0a89">
ChangeLog.txt
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<li class="file-stats">
<a href="#09de00a2f5fb0a5a61122f0d649401a900bbb57b">
scripts/last-postmask
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<li class="file-stats">
<a href="#37ef3bfb2f847a5a03a3da6d653afee2ea7e05b0">
scripts/last-train
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<li class="file-stats">
<a href="#69737f84c540417aafef4e696f66adcc9f92fa66">
src/version.hh
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<h4>Changes:</h4>
<li id="57bf262130f956caf76c405086f0815caf4e0a89">
<a href="https://salsa.debian.org/med-team/last-align/commit/1114371359a004321568097e7d1c60eeb26e63c2#57bf262130f956caf76c405086f0815caf4e0a89"><strong>ChangeLog.txt</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">2020-01-20 Martin C. Frith <Martin C. Frith></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * scripts/last-postmask, test/last-postmask-test.out, test/last-</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> postmask-test.sh:</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> last-postmask: fix crash on length-1 DB name</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> [1015a8df8312] [tip]</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * scripts/last-train:</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> last-train: fix occasional crashes since v1020</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> [b6a6f4a9d738]</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">2019-12-23 Martin C. Frith <Martin C. Frith></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> * src/Alignment.cc, src/GappedXdropAligner.hh,</span>
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<td class="diff-line-num new_line" data-linenumber="15" 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="LC15" class="line" lang="plaintext"> src/GappedXdropAlignerDna.cc, src/mcf_simd.hh:</span>
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<td class="diff-line-num new_line" data-linenumber="16" 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="LC16" class="line" lang="plaintext"> Make it usable without SSE/SIMD</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"> [4270e27518ca]<span class="idiff left right"> [tip]</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> [4270e27518ca]</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_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">2019-12-20 Martin C. Frith <Martin C. Frith></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/last-align/commit/1114371359a004321568097e7d1c60eeb26e63c2#09de00a2f5fb0a5a61122f0d649401a900bbb57b"><strong>scripts/last-postmask</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">@@ -111,7 +111,7 @@ def doOneFile(lines):</td>
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">"B="</span><span class="p">):</span> <span class="n" style="color: #333;">bIns</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">:])</span></span>
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112
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">"e="</span><span class="p">):</span> <span class="n" style="color: #333;">minScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">:])</span></span>
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113
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113
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">"S="</span><span class="p">):</span> <span class="n" style="color: #333;">strandParam</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">:])</span></span>
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114
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">nf</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;"><span class="idiff left right">1</span></span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">,</span> <span class="n" style="color: #333;">fields</span><span class="p">))</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">nf</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;"><span class="idiff left right">2</span></span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">,</span> <span class="n" style="color: #333;">fields</span><span class="p">))</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>
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115
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115
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="python"> <span class="n" style="color: #333;">colHeads</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:]</span></span>
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116
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116
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">nf</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">colHeads</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">2</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>
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117
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117
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="python"> <span class="n" style="color: #333;">rowHeads</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="382" 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">@@ -382,7 +382,7 @@ def balancedScale(nearScale, *args):</td>
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382
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382
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<pre style="margin: 0;"> <span id="LC382" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">abs</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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383
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383
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<pre style="margin: 0;"> <span id="LC383" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">nearScale</span></span>
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384
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384
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<pre style="margin: 0;"> <span id="LC384" class="line" lang="python"> <span class="n" style="color: #333;">oldLower</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">oldUpper</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nearScale</span></span>
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385
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<pre style="margin: 0;">-<span id="LC385" class="line" lang="python"> <span class="k" style="font-weight: 600;">while</span> <span class="bp" style="color: #999;"><span class="idiff left">True</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right"># xxx</span></span></span>
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385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="python"> <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;"><span class="idiff left">oldUpper</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">nearScale</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right"># xxx ???</span></span></span>
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386
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386
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<pre style="margin: 0;"> <span id="LC386" class="line" lang="python"> <span class="n" style="color: #333;">newLower</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">oldLower</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">bump</span></span>
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387
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387
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<pre style="margin: 0;"> <span id="LC387" class="line" lang="python"> <span class="n" style="color: #333;">lowerValue</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scoreImbalance</span><span class="p">(</span><span class="n" style="color: #333;">newLower</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">)</span></span>
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388
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388
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<pre style="margin: 0;"> <span id="LC388" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">lowerValue</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="p">(</span><span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">):</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="395" 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">@@ -395,6 +395,7 @@ def balancedScale(nearScale, *args):</td>
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395
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395
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<pre style="margin: 0;"> <span id="LC395" class="line" lang="python"> <span class="n" style="color: #333;">func</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scoreImbalance</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">negScoreImbalance</span></span>
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<pre style="margin: 0;"> <span id="LC396" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">rootOfIncreasingFunction</span><span class="p">(</span><span class="n" style="color: #333;">func</span><span class="p">,</span> <span class="n" style="color: #333;">oldUpper</span><span class="p">,</span> <span class="n" style="color: #333;">newUpper</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC397" class="line" lang="python"> <span class="n" style="color: #333;">oldUpper</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">newUpper</span></span>
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="mf" style="color: #099;">0.0</span></span>
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<pre style="margin: 0;"> <span id="LC399" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC400" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">scoresAndScale</span><span class="p">(</span><span class="n" style="color: #333;">originalScale</span><span class="p">,</span> <span class="n" style="color: #333;">matParams</span><span class="p">,</span> <span class="n" style="color: #333;">delRatios</span><span class="p">,</span> <span class="n" style="color: #333;">insRatios</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC401" class="line" lang="python"> <span class="k" style="font-weight: 600;">while</span> <span class="bp" style="color: #999;">True</span><span class="p">:</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -402,10 +403,11 @@ def scoresAndScale(originalScale, matParams, delRatios, insRatios):</td>
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402
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<pre style="margin: 0;"> <span id="LC403" class="line" lang="python"> <span class="n" style="color: #333;">delCosts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapCostsFromProbRatios</span><span class="p">(</span><span class="n" style="color: #333;">originalScale</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">delRatios</span><span class="p">)</span></span>
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403
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404
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<pre style="margin: 0;"> <span id="LC404" class="line" lang="python"> <span class="n" style="color: #333;">insCosts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapCostsFromProbRatios</span><span class="p">(</span><span class="n" style="color: #333;">originalScale</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">insRatios</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC405" class="line" lang="python"> <span class="n" style="color: #333;">scale</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">balancedScale</span><span class="p">(</span><span class="n" style="color: #333;">originalScale</span><span class="p">,</span> <span class="n" style="color: #333;">matScores</span><span class="p">,</span> <span class="n" style="color: #333;">delCosts</span><span class="p">,</span> <span class="n" style="color: #333;">insCosts</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC405" class="line" lang="python"> <span class="n" style="color: #333;">rowFreqs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">homogeneousLetterFreqs</span><span class="p">(</span><span class="n" style="color: #333;">scale</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">matScores</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC406" class="line" lang="python"> <span class="n" style="color: #333;">colFreqs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">homogeneousLetterFreqs</span><span class="p">(</span><span class="n" style="color: #333;">scale</span><span class="p">,</span> <span class="n" style="color: #333;">matScores</span><span class="p">)</span></span>
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407
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<pre style="margin: 0;">-<span id="LC407" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">all</span><span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">rowFreqs</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">colFreqs</span><span class="p">):</span></span>
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408
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<pre style="margin: 0;">-<span id="LC408" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">matScores</span><span class="p">,</span> <span class="n" style="color: #333;">delCosts</span><span class="p">,</span> <span class="n" style="color: #333;">insCosts</span><span class="p">,</span> <span class="n" style="color: #333;">scale</span></span>
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">scale</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="python"> <span class="n" style="color: #333;">rowFreqs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">homogeneousLetterFreqs</span><span class="p">(</span><span class="n" style="color: #333;">scale</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">matScores</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="python"> <span class="n" style="color: #333;">colFreqs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">homogeneousLetterFreqs</span><span class="p">(</span><span class="n" style="color: #333;">scale</span><span class="p">,</span> <span class="n" style="color: #333;">matScores</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">all</span><span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">rowFreqs</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">colFreqs</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">matScores</span><span class="p">,</span> <span class="n" style="color: #333;">delCosts</span><span class="p">,</span> <span class="n" style="color: #333;">insCosts</span><span class="p">,</span> <span class="n" style="color: #333;">scale</span></span>
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411
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<pre style="margin: 0;"> <span id="LC411" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"# the integer-rounded scores are too inaccurate: "</span></span>
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410
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412
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<pre style="margin: 0;"> <span id="LC412" class="line" lang="python"> <span class="s" style="color: #d14;">"doubling the scale"</span><span class="p">)</span></span>
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411
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413
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<pre style="margin: 0;"> <span id="LC413" class="line" lang="python"> <span class="n" style="color: #333;">originalScale</span> <span class="o" style="font-weight: 600;">*=</span> <span class="mi" style="color: #099;">2</span></span>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="cpp"><span class="s" style="color: #d14;">"104<span class="idiff left right">5</span>"</span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="cpp"><span class="s" style="color: #d14;">"104<span class="idiff left right">7</span>"</span></span></pre>
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