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<h3>
Michael R. Crusoe pushed to branch master
at <a href="https://salsa.debian.org/med-team/snap-aligner">Debian Med / snap-aligner</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/snap-aligner/-/commit/c6374c05b995389fb3a87961eec0d25995565c80">c6374c05</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-07-09T11:08:18+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">update my email address
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/snap-aligner/-/commit/616a8ba698e6ce9c93e99002c227da38dd0c19a1">616a8ba6</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-07-09T11:11:26+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add upstream repository to metadata
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/snap-aligner/-/commit/dbd8ee1605499927403168286d444a4ee8728aec">dbd8ee16</a></strong>
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<span>by Michael R. Crusoe</span>
<i>at 2020-07-09T11:13:51+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed another spelling error
</pre>
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<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#e4c19aed51618bf0c7ebd03189c67e422f84d4eb">
debian/patches/spelling
</a>
</li>
<li class="file-stats">
<a href="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">
debian/upstream/metadata
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</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/snap-aligner/-/compare/dbce13f7e84a1ad8f51d322a7be114d7c023a9c3...dbd8ee1605499927403168286d444a4ee8728aec#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="diff-line-num unfold js-unfold old_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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -15,7 +15,9 @@ snap-aligner (1.0~beta.18+dfsg-4) unstable; urgency=medium</td>
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<td class="diff-line-num old_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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<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"> * Remove trailing whitespace in debian/copyright (routine-update)</span>
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<td class="diff-line-num old_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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<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"> * Add salsa-ci file (routine-update)</span>
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<td class="diff-line-num old_line" data-linenumber="17" 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="17" 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="LC17" class="line" lang="plaintext"> * Rules-Requires-Root: no (routine-update)</span>
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<td class="diff-line-num old old_line" data-linenumber="18" 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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<td class="diff-line-num new_line old" data-linenumber="18" 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="LC18" class="line" lang="plaintext"> * Set upstream metadata fields: Bug-Database, Bug-Submit.</span>
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<td class="diff-line-num new old_line" data-linenumber="19" 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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<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">
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,</span>
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<td class="diff-line-num new old_line" data-linenumber="19" 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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<td class="diff-line-num new new_line" data-linenumber="19" 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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> Repository-Browse</span>
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<td class="diff-line-num new old_line" data-linenumber="19" 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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<td class="diff-line-num new new_line" data-linenumber="20" 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="LC20" class="line" lang="plaintext"> * Fixed another spelling error</span>
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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"> -- Michael R. Crusoe <crusoe@debian.org> Thu, 09 Jul 2020 11:00:43 +0200</span>
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<td class="diff-line-num new_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"></span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/snap-aligner/-/compare/dbce13f7e84a1ad8f51d322a7be114d7c023a9c3...dbd8ee1605499927403168286d444a4ee8728aec#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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="plaintext">Source: snap-aligner</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Uploaders: Michael R. Crusoe <<span class="idiff left right">michael.crusoe@gmail.com</span>>,</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Uploaders: Michael R. Crusoe <<span class="idiff left right">crusoe@debian.org</span>>,</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> Pranav Ballaney <ballaneypranav@gmail.com></span>
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<td class="diff-line-num old_line" data-linenumber="5" 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="LC5" class="line" lang="plaintext">Section: science</span>
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<td class="diff-line-num old_line" data-linenumber="6" 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="LC6" class="line" lang="plaintext">Priority: optional</span>
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<li id="e4c19aed51618bf0c7ebd03189c67e422f84d4eb">
<a href="https://salsa.debian.org/med-team/snap-aligner/-/compare/dbce13f7e84a1ad8f51d322a7be114d7c023a9c3...dbd8ee1605499927403168286d444a4ee8728aec#e4c19aed51618bf0c7ebd03189c67e422f84d4eb"><strong>debian/patches/spelling</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">@@ -30,3 +30,14 @@ Forwarded: https://github.com/amplab/snap/pull/66</td>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="diff"> " following type specifiers (which are case sensitive):\n"</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="diff"> " -fastq\n"</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="diff"> " -compressedFastq\n"</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- snap-aligner.orig/SNAPLib/GenomeIndex.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ snap-aligner/SNAPLib/GenomeIndex.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="p">@@ -1284,7 +1284,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> WriteErrorMessage("HashTable[%d] has %lld used elements\n",j,(_int64)index->hashTables[j]->GetUsedElementCount());</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> WriteErrorMessage("IndexBuilder: exceeded size of hash table %d.\n"</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- "If you're indexing a non-human genome, make sure not to pass the -hg19 option. Otheriwse, use -exact or increase slack with -h.\n",</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "If you're indexing a non-human genome, make sure not to pass the -hg19 option. Otherwise, use -exact or increase slack with -h.\n",</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> whichHashTable);</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> soft_exit(1);</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> }</span></pre>
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<a href="https://salsa.debian.org/med-team/snap-aligner/-/compare/dbce13f7e84a1ad8f51d322a7be114d7c023a9c3...dbd8ee1605499927403168286d444a4ee8728aec#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</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="plaintext">Bug-Database: https://github.com/amplab/snap/issues</span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Bug-Submit: https://github.com/amplab/snap/issues/new</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Repository-Browse: https://github.com/amplab/snap</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Repository: https://github.com/amplab/snap.git</span>
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3
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Reference:</span>
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4
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> Author: ></span>
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5
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> Matei Zaharia and William J. Bolosky and Kristal Curtis and Armando</span>
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