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<h3>
Antoni Villalonga pushed to branch master
at <a href="https://salsa.debian.org/med-team/pairtools">Debian Med / pairtools</a>
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<h4>
Commits:
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<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/pairtools/-/commit/4997f0f9baa5272bcbdf6897994bfd3413346df3">4997f0f9</a></strong>
<div>
<span>by Antoni Villalonga</span>
<i>at 2020-06-20T02:45:11+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Include d/upstream/metadata
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<strong><a href="https://salsa.debian.org/med-team/pairtools/-/commit/749e2f0c5d806b9cfcf3a61a31c18d87b07976be">749e2f0c</a></strong>
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<span>by Antoni Villalonga</span>
<i>at 2020-06-20T02:45:11+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New -examples package
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<h4>5 changed files:</h4>
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debian/README.test
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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debian/python3-pairtools-examples.install
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debian/python3-pairtools.docs
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debian/upstream/metadata
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<h4>Changes:</h4>
<li id="f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
<a href="https://salsa.debian.org/med-team/pairtools/-/compare/fe90c3d0c60319c3ce5394ab5a478af6e63fd861...749e2f0c5d806b9cfcf3a61a31c18d87b07976be#f6a99a1e522a0f5ca122fd9818a9d8536ea59942"><strong>debian/README.test</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nx">Notes</span> <span class="nx">on</span> <span class="nx">how</span> <span class="nx">this</span> <span class="nx">package</span> <span class="nx">can</span> <span class="nx">be</span> <span class="nx">tested</span><span class="o" style="font-weight: 600;">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2" 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">
2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="php"><span class="err" style="color: #a61717; background-color: #e3d2d2;">────────────────────────────────────────</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3" 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">
3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="php"></span>
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<td class="diff-line-num new new_line" data-linenumber="4" 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="LC4" class="line" lang="php"><span class="nx">This</span> <span class="nx">package</span> <span class="nx">can</span> <span class="nx">be</span> <span class="nx">tested</span> <span class="nx">by</span> <span class="nx">running</span> <span class="nx">the</span> <span class="nx">provided</span> <span class="nx">test</span><span class="o" style="font-weight: 600;">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5" 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">
5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="php"> <span class="nx">apt</span> <span class="nx">install</span> <span class="nx">python3</span><span class="o" style="font-weight: 600;">-</span><span class="nx">pairtools</span><span class="o" style="font-weight: 600;">-</span><span class="nx">examples</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="6" 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">
6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="php"> <span class="nx">cd</span> <span class="o" style="font-weight: 600;">/</span><span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">doc</span><span class="o" style="font-weight: 600;">/</span><span class="nx">python3</span><span class="o" style="font-weight: 600;">-</span><span class="nx">pairtools</span><span class="o" style="font-weight: 600;">/</span><span class="nx">examples</span><span class="o" style="font-weight: 600;">/</span><span class="nx">tests</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nx">nosetests3</span></span>
</pre>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="php"></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="php"><span class="nx">in</span> <span class="nx">order</span> <span class="nx">to</span> <span class="nx">confirm</span> <span class="nx">its</span> <span class="nx">integrity</span><span class="o" style="font-weight: 600;">.</span></span></pre>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/pairtools/-/compare/fe90c3d0c60319c3ce5394ab5a478af6e63fd861...749e2f0c5d806b9cfcf3a61a31c18d87b07976be#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="58" 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="58" 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">@@ -58,3 +58,24 @@ Description: Process sequencing data from a Hi-C experiment (debug build)</td>
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58
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58
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="plaintext"> - Generate extensive statistics of Hi-C datasets</span>
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<td class="diff-line-num old_line" data-linenumber="59" 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="59" 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">
59
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="plaintext"> - Select Hi-C pairs given flexibly defined criteria</span>
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<td class="diff-line-num old_line" data-linenumber="60" 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="60" 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="LC60" class="line" lang="plaintext"> - Restore .sam alignments from Hi-C pairs</span>
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<td class="diff-line-num new old_line" data-linenumber="61" 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="61" 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="LC61" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="62" 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="LC62" class="line" lang="plaintext">Package: python3-pairtools-examples</span>
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<td class="diff-line-num new old_line" data-linenumber="61" 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="63" 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="LC63" class="line" lang="plaintext">Architecture: any</span>
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<td class="diff-line-num new new_line" data-linenumber="64" 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="LC64" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<td class="diff-line-num new new_line" data-linenumber="65" 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="LC65" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">Enhances: python3-pairtools</span>
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<td class="diff-line-num new new_line" data-linenumber="67" 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="LC67" class="line" lang="plaintext">Description: Process sequencing data from a Hi-C experiment (examples)</span>
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<td class="diff-line-num new new_line" data-linenumber="68" 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="LC68" class="line" lang="plaintext"> Simple and fast command-line framework to process sequencing data from a Hi-C</span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext"> experiment.</span>
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70
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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"> Process pair-end sequence alignments and perform the following operations:</span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext"> .</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext"> - Detect ligation junctions (a.k.a. Hi-C pairs) in aligned paired-end</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext"> sequences of Hi-C DNA molecules</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext"> - Sort .pairs files for downstream analyses</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext"> - Detect, tag and remove PCR/optical duplicates</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext"> - Generate extensive statistics of Hi-C datasets</span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext"> - Select Hi-C pairs given flexibly defined criteria</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext"> - Restore .sam alignments from Hi-C pairs</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext"> This package contains some examples</span></pre>
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<a href="https://salsa.debian.org/med-team/pairtools/-/compare/fe90c3d0c60319c3ce5394ab5a478af6e63fd861...749e2f0c5d806b9cfcf3a61a31c18d87b07976be#30ce1aa73864043896c6c66ff62fea7bd1cacd14"><strong>debian/python3-pairtools-examples.install</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nx">tests</span><span class="o" style="font-weight: 600;">/*.</span><span class="nx">py</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">doc</span><span class="o" style="font-weight: 600;">/</span><span class="nx">python3</span><span class="o" style="font-weight: 600;">-</span><span class="nx">pairtools</span><span class="o" style="font-weight: 600;">/</span><span class="nx">examples</span><span class="o" style="font-weight: 600;">/</span><span class="nx">tests</span><span class="o" style="font-weight: 600;">/</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="php"><span class="nx">tests</span><span class="o" style="font-weight: 600;">/</span><span class="nx">data</span><span class="o" style="font-weight: 600;">/*</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">doc</span><span class="o" style="font-weight: 600;">/</span><span class="nx">python3</span><span class="o" style="font-weight: 600;">-</span><span class="nx">pairtools</span><span class="o" style="font-weight: 600;">/</span><span class="nx">examples</span><span class="o" style="font-weight: 600;">/</span><span class="nx">tests</span><span class="o" style="font-weight: 600;">/</span><span class="nx">data</span></span></pre>
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<a href="https://salsa.debian.org/med-team/pairtools/-/compare/fe90c3d0c60319c3ce5394ab5a478af6e63fd861...749e2f0c5d806b9cfcf3a61a31c18d87b07976be#9d17cccfa99020af6e0f896b0179adf2b894ba71"><strong>debian/python3-pairtools.docs</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/README.test</span></pre>
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<a href="https://salsa.debian.org/med-team/pairtools/-/compare/fe90c3d0c60319c3ce5394ab5a478af6e63fd861...749e2f0c5d806b9cfcf3a61a31c18d87b07976be#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Repository-Browse: https://github.com/mirnylab/pairtools</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Repository: https://github.com/mirnylab/pairtools.git</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Bug-Database: https://github.com/mirnylab/pairtools/issues</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Bug-Submit: https://github.com/mirnylab/pairtools/issues/new</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">Registry:</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> - Name: conda:bioconda</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> Entry: pairtools</span></pre>
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