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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/last-align">Debian Med / last-align</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/last-align/-/commit/08c0f517b26d8aba14bb4844b279baabf9d07c24">08c0f517</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-01-10T09:43:12+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1257</pre>
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<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#561b88e19de321ca62c7590bbb350765fb110905">
README.rst
</a>
</li>
<li class="file-stats">
<a href="#3005ac7967e4a8278470a34d68f44dcd2b1b63cd">
doc/last-dotplot.rst
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<li class="file-stats">
<a href="#0c0610d12d971107a85160c6a927e94a1062a01a">
makefile
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<li class="file-stats">
<a href="#58ea1bfb97fa00a98b822ca930a2003aafdcc2b2">
src/makefile
</a>
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<h4>Changes:</h4>
<li id="561b88e19de321ca62c7590bbb350765fb110905">
<a href="https://salsa.debian.org/med-team/last-align/-/commit/08c0f517b26d8aba14bb4844b279baabf9d07c24#561b88e19de321ca62c7590bbb350765fb110905"><strong>README.rst</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">@@ -23,8 +23,9 @@ Usage</td>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">-----</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">Please see the cookbook_. **Warning:** this documentation may not</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext">apply to older versions of LAST! You can see your version with</span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext">``lastal --version``.</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">apply to older versions of LAST! You can see your version with::</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> lastal --version</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext">Install</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext">-------</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="39" 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">@@ -38,8 +39,16 @@ into the downloaded directory and type::</td>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext">This assumes you have a C++ compiler. On Linux, you might need to</span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext">install a package called "g++". On Mac, you might need to install</span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext">command-line developer tools. On Windows, you might need to install</span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="plaintext">Cygwin. (It's possible to specify a compiler like this:</span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext">``make CXX=MyOtherCompiler``.)</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">Cygwin. You might also need to install something like "zlib-devel".</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">For ARM CPUs, the default "make" seems to work in some cases but not</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">others (sigh). This seems to be good for ARM::</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"> make CXXFLAGS="-mcpu=native -O3 -pthread"</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">It's possible to specify a compiler like this: ``make CXX=MyOtherCompiler``.</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">If you re-run ``make`` in different ways, it may be good to do ``make clean``</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">first, to remove any previously-made files.</span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="plaintext">The programs are in the ``bin`` directory. For convenient usage, set</span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="plaintext">up your computer to find them automatically. Some possible ways:</span>
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<a href="https://salsa.debian.org/med-team/last-align/-/commit/08c0f517b26d8aba14bb4844b279baabf9d07c24#3005ac7967e4a8278470a34d68f44dcd2b1b63cd"><strong>doc/last-dotplot.rst</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">@@ -159,10 +159,10 @@ Options ``-a`` and ``-b`` can read annotations in these formats:</td>
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="plaintext">* AGP_, gap.txt: Unsequenced gaps are shown, but only if the gap</span>
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="plaintext"> covers at least one whole pixel.</span>
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="plaintext">You can use these options multiple times, e.g.<span class="idiff left right"> ``-a stuff.bed -a</span></span>
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="plaintext">more.bed -a rmsk.txt``. Annotations look good only<span class="idiff left right"> if reasonably</span></span>
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="plaintext">sparse, e.g. you can't sensibly view 20000 gene<span class="idiff left right"> annotations in one</span></span>
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="plaintext">small dotplot.</span>
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="plaintext">You can use these options multiple times, e.g.</span>
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="plaintext"><span class="idiff left right">``-a stuff.bed -a </span>more.bed -a rmsk.txt``. Annotations look good only</span>
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="plaintext"><span class="idiff left right">if reasonably </span>sparse, e.g. you can't sensibly view 20000 gene</span>
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="plaintext"><span class="idiff left right">annotations in one </span>small dotplot.</span>
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="plaintext">Choosing sequences</span>
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="plaintext">------------------</span>
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<a href="https://salsa.debian.org/med-team/last-align/-/commit/08c0f517b26d8aba14bb4844b279baabf9d07c24#0c0610d12d971107a85160c6a927e94a1062a01a"><strong>makefile</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="make"><span class="nv" style="color: #008080;">CXXFLAGS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: #000080;">-msse4</span> <span class="nt" style="color: #000080;">-O3</span> <span class="nt" style="color: #000080;">-std</span><span class="o" style="font-weight: 600;">=</span>c++11 <span class="nt" style="color: #000080;">-pthread</span><span class="idiff left"> </span><span class="nt" style="color: #000080;"><span class="idiff right">-DHAS_CXX_THREADS</span></span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="make"><span class="nv" style="color: #008080;">CXXFLAGS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: #000080;">-msse4</span> <span class="nt" style="color: #000080;">-O3</span> <span class="nt" style="color: #000080;">-std</span><span class="o" style="font-weight: 600;">=</span>c++11 <span class="nt" style="color: #000080;">-pthread</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="make"><span class="nl">all</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">cd </span>src <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$(MAKE)</span> <span class="nv" style="color: #008080;">CXXFLAGS</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$(CXXFLAGS)</span><span class="s2" style="color: #d14;">"</span></span>
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<a href="https://salsa.debian.org/med-team/last-align/-/commit/08c0f517b26d8aba14bb4844b279baabf9d07c24#58ea1bfb97fa00a98b822ca930a2003aafdcc2b2"><strong>src/makefile</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="make"><span class="nv" style="color: #008080;">CXXFLAGS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: #000080;">-msse4</span> <span class="nt" style="color: #000080;">-O3</span> <span class="nt" style="color: #000080;">-Wall</span> <span class="nt" style="color: #000080;">-g</span> <span class="nt" style="color: #000080;">-std</span><span class="o" style="font-weight: 600;">=</span>c++11 <span class="nt" style="color: #000080;">-pthread</span><span class="idiff left"> </span><span class="nt" style="color: #000080;"><span class="idiff right">-DHAS_CXX_THREADS</span></span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="make"><span class="nv" style="color: #008080;">CXXFLAGS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: #000080;">-msse4</span> <span class="nt" style="color: #000080;">-O3</span> <span class="nt" style="color: #000080;">-Wall</span> <span class="nt" style="color: #000080;">-g</span> <span class="nt" style="color: #000080;">-std</span><span class="o" style="font-weight: 600;">=</span>c++11 <span class="nt" style="color: #000080;">-pthread</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;"># -fomit-frame-pointer ?</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="make"></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;"># The number of symbol types that we can keep in sequences (e.g. 20</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;"># amino acids, plus ambiguous ones, in upper & lower case, plus one</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;"># delimiter):</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="make"><span class="nv" style="color: #008080;">ALPHABET_CAPACITY</span> <span class="o" style="font-weight: 600;">=</span> 66</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="make"><span class="nv" style="color: #008080;">CPPF</span> <span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: #000080;">-DALPHABET_CAPACITY</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$(ALPHABET_CAPACITY)</span> <span class="nv" style="color: #008080;">$(CPPFLAGS)</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="make"><span class="nv" style="color: #008080;">CPPF</span> <span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: #000080;">-DALPHABET_CAPACITY</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$(ALPHABET_CAPACITY)</span> <span class="nt" style="color: #000080;"><span class="idiff left">-DHAS_CXX_THREADS</span></span><span class="idiff right"> </span><span class="nv" style="color: #008080;">$(CPPFLAGS)</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="make"><span class="nv" style="color: #008080;">CFLAGS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: #000080;">-Wall</span> <span class="nt" style="color: #000080;">-O2</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="make"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -143,7 +143,7 @@ ScoreMatrixData.hh: ../data/*.mat</td>
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="make"> ../build/mat-inc.sh ../data/<span class="k" style="font-weight: 600;">*</span>.mat <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$@</span></span>
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="make"><span class="nv" style="color: #008080;">VERSION1</span> <span class="o" style="font-weight: 600;">=</span> git describe <span class="nt" style="color: #000080;">--dirty</span></span>
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="make"><span class="nv" style="color: #008080;">VERSION2</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">' (HEAD -> main, tag: 125<span class="idiff left right">6</span>) '</span> | <span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/.*tag: *//'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/[,) ].*//'</span></span>
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="make"><span class="nv" style="color: #008080;">VERSION2</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">' (HEAD -> main, tag: 125<span class="idiff left right">7</span>) '</span> | <span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/.*tag: *//'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/[,) ].*//'</span></span>
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="make"><span class="nv" style="color: #008080;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="se" style="color: #d14;">\"</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">test</span> <span class="nt" style="color: #000080;">-e</span> ../.git <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$(VERSION1)</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">$(VERSION2)</span><span class="sb" style="color: #d14;">`</span><span class="se" style="color: #d14;">\"</span></span>
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