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<h3>
Shayan Doust pushed to branch master
at <a href="https://salsa.debian.org/med-team/mindthegap">Debian Med / mindthegap</a>
</h3>
<h4>
Commits:
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<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/mindthegap/-/commit/171decd0b1a305ab7492f915fd67a23c5572d545">171decd0</a></strong>
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<span>by Shayan Doust</span>
<i>at 2020-06-21T17:38:24+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add missing (test) dependency and fix test
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<h4>2 changed files:</h4>
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#c097af3a113f6c53daa9a4e2669e62e0732f062a">
debian/patches/modify_tests_for_autopkgtest.patch
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/mindthegap/-/commit/171decd0b1a305ab7492f915fd67a23c5572d545#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="18" 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="18" 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">@@ -18,7 +18,7 @@ Package: mindthegap</td>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Architecture: any</span>
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<td class="diff-line-num old_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">Depends: ${shlibs:Depends},</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> libgatbcore<span class="idiff left right">2</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> libgatbcore<span class="idiff left right">3</span></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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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">Description: performs detection and assembly of DNA insertion variants in NGS read datasets</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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<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"> Designed to call insertions of any size, whether they are novel or</span>
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<td class="diff-line-num old_line" data-linenumber="24" 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="LC24" class="line" lang="plaintext"> duplicated, homozygous or heterozygous in the donor genome. It takes as</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="33" 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="33" 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">@@ -33,7 +33,8 @@ Description: performs detection and assembly of DNA insertion variants in NGS re</td>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext">Package: mindthegap-examples</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext">Depends: ${misc:Depends},</span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="plaintext"> python3</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> python3,</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> bsdextrautils | bsdmainutils (<< 12.1.1~)</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext">Recommends: mindthegap</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext">Description: optional scripts and example resources for mindthegap</span>
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<td class="diff-line-num old_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">
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<td class="diff-line-num new_line" data-linenumber="40" 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="LC40" class="line" lang="plaintext"> Designed to call insertions of any size, whether they are novel or</span>
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<li id="c097af3a113f6c53daa9a4e2669e62e0732f062a">
<a href="https://salsa.debian.org/med-team/mindthegap/-/commit/171decd0b1a305ab7492f915fd67a23c5572d545#c097af3a113f6c53daa9a4e2669e62e0732f062a"><strong>debian/patches/modify_tests_for_autopkgtest.patch</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff"><span class="p">Description: Fix upstream pre-existing test scripts</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"> This will ensure that autopkgtest can invoke these scripts. They need to be modified to remove any mindthegap binary checks that the upstream author has put in place as well as ensuring the script invokes the global MindTheGap command</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="p">Author: Shayan Doust <hello@shayandoust.me></span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="p">Last-Update: 20<span class="idiff left right">19-07-09</span></span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Last-Update: 20<span class="idiff left right">20-06-21</span></span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff">--- mindthegap.orig/test/simple_full_test.sh</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ mindthegap/test/simple_full_test.sh</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="31" 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="31" 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">@@ -31,6 +31,15 @@ Last-Update: 2019-07-09</td>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-${bindir}/MindTheGap find -in ../data/reads_r1.fastq,../data/reads_r2.fastq -ref ../data/reference.fasta -out $outputPrefix >$outputPrefix.out -nb-cores 1 2> /dev/null</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+MindTheGap find -in ../data/reads_r1.fastq,../data/reads_r2.fastq -ref ../data/reference.fasta -out $outputPrefix >$outputPrefix.out -nb-cores 1 2> /dev/null</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> ################################################################################</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> # we check the results </span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="p">@@ -77,7 +64,7 @@</span></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"> # we launch the find module with bed option</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> ################################################################################</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-${bindir}/MindTheGap find -in ../data/reads_r1.fastq,../data/reads_r2.fastq -ref ../data/reference.fasta -bed ${goldPrefix}.bed -out ${outputPrefix}_bed >${outputPrefix}_bed.out -nb-cores 1 2> /dev/null</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+MindTheGap find -in ../data/reads_r1.fastq,../data/reads_r2.fastq -ref ../data/reference.fasta -bed ${goldPrefix}.bed -out ${outputPrefix}_bed >${outputPrefix}_bed.out -nb-cores 1 2> /dev/null</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="diff"> ################################################################################</span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="diff"> # we check the results </span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="diff"><span class="p">@@ -121,7 +108,7 @@</span></span>
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