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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/libmmmulti">Debian Med / libmmmulti</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/libmmmulti/-/commit/f7ea422597daa7f046cccd9d2f4582da5f5d087c">f7ea4225</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-10-27T17:19:15+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Separate tool from architecture all library
</pre>
</li>
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<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#a050623b065e4fd7f5e1cf1c1ec57af275a12d85">
debian/libmmmulti-dev.install
</a>
</li>
<li class="file-stats">
<a href="#c86eb5d32cc409b4815f8a8f62e8bcb2b43e594b">
<span class="new-file">
+
debian/mmmulti.install
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</a>
</li>
<li class="file-stats">
<a href="#08821d2708975b4aeb59ae62f449dda769823a86">
debian/manpages
→
debian/mmmulti.manpages
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/libmmmulti/-/commit/f7ea422597daa7f046cccd9d2f4582da5f5d087c#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="21" 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="21" 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">@@ -21,10 +21,10 @@ Rules-Requires-Root: no</td>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="22" 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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<td class="diff-line-num new_line" data-linenumber="22" 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="LC22" class="line" lang="plaintext">Package: libmmmulti-dev</span>
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<td class="diff-line-num old_line" data-linenumber="23" 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="LC23" class="line" lang="plaintext">Section: libdevel</span>
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<td class="diff-line-num old old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext">Architecture: a<span class="idiff left right">ny</span></span>
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<td class="diff-line-num new old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">Architecture: a<span class="idiff left right">ll</span></span>
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<td class="diff-line-num old_line" data-linenumber="25" 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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<td class="diff-line-num new_line" data-linenumber="25" 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="LC25" class="line" lang="plaintext">Multi-Arch: foreign</span>
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<td class="diff-line-num old_line" data-linenumber="26" 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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<td class="diff-line-num new_line" data-linenumber="26" 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="LC26" class="line" lang="plaintext">Depends: ${shlibs:Depends}, ${misc:Depends}</span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext">Description: header <span class="idiff left right">files for mmmulti library</span></span>
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<td class="diff-line-num new old_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">Description: header <span class="idiff left right">only library for mmmulti</span></span>
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<td class="diff-line-num old_line" data-linenumber="28" 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="LC28" class="line" lang="plaintext"> Sometimes you have a lot of plain-old data, but you need random access</span>
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<td class="diff-line-num old_line" data-linenumber="29" 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="LC29" class="line" lang="plaintext"> to it. These header-only classes combine memory-mapped files with</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"> high-performance parallel sorting and appropriate indexing strategies</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="50" 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="50" 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">@@ -50,3 +50,29 @@ Description: header files for mmmulti library</td>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="plaintext"> scale to extremely large problem sizes, limited only by available disk</span>
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<td class="diff-line-num old_line" data-linenumber="51" 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="LC51" class="line" lang="plaintext"> space. Although performance is much slower than an in-memory structure,</span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="plaintext"> it is virtually guaranteed to be able to complete the compute.</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">Package: mmmulti</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">Architecture: any</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">Multi-Arch: foreign</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">Depends: ${shlibs:Depends}, ${misc:Depends}</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">Description: memory backed multimap</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext"> This implements a memory backed multimap intended for use where:</span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"> * your keys are integers, or can be mapped to dense range of integers,</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext"> * the memory mapped file is on fast storage, like an SSD (although</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext"> this is not a requirement),</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext"> * you have arbitrary values of fixed size (e.g. structs, other POD</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext"> types) that can be sorted,</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext"> * you don't need dynamic updates of the table,</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext"> * and you are likely to run out of memory of you use a traditional</span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext"> map or hash table,</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext"> * but you can handle approximately 1 bit per record in RAM.</span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext"> .</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext"> These may seem to be very specific, but many problems can be mapped into</span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext"> a dense integer set. mmmulti::map developed first as a data structure</span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext"> to support seqwish, which uses it to generate precise variation graphs</span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext"> from pairwise alignments between collections of sequences. As this</span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext"> multimap forms a key data processing kernel in the algorithm, it can</span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext"> scale to extremely large problem sizes, limited only by available disk</span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext"> space. Although performance is much slower than an in-memory structure,</span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext"> it is virtually guaranteed to be able to complete the compute.</span></pre>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="php"><span class="n" style="color: #333;">bin</span><span class="o" style="font-weight: 600;">/*</span> <span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">bin</span></span>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="php"><span class="n" style="color: #333;">src</span><span class="o" style="font-weight: 600;">/*.</span><span class="n" style="color: #333;">hpp</span> <span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="k" style="font-weight: 600;">include</span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="n" style="color: #333;">bin</span><span class="o" style="font-weight: 600;">/*</span> <span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">bin</span></span></pre>
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