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<h3>
Steffen Möller pushed to branch master
at <a href="https://salsa.debian.org/med-team/bcbio">Debian Med / bcbio</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/bcbio/-/commit/500c1dd9c71ac9ac534b689a328b6e4d959ad08f">500c1dd9</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2021-05-07T22:31:43+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Removed obsolete patch
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bcbio/-/commit/793c330de6805efac17fc4527d388778f5f52081">793c330d</a></strong>
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<span>by Steffen Moeller</span>
<i>at 2021-05-07T23:17:42+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update of dependencies
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<h4>5 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#f168b81935360ddcf2dd0f2d4b98b8603829060f">
debian/README.Debian
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#0077a2c2838f7524dc36a2824fe4af986d35f032">
<span class="deleted-file">
−
debian/patches/collectionsAbc.patch
</span>
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
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<h4>Changes:</h4>
<li id="f168b81935360ddcf2dd0f2d4b98b8603829060f">
<a href="https://salsa.debian.org/med-team/bcbio/-/compare/cd8feac301800694e286f39f4104597b70d1d857...793c330de6805efac17fc4527d388778f5f52081#f168b81935360ddcf2dd0f2d4b98b8603829060f"><strong>debian/README.Debian</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">@@ -5,4 +5,7 @@ This package builds and tests fine, but the documentation is not yet packaged.</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Please be aware of related Debian packages for toil and cwltool.</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">The package "tophat" was removed from Debian since the developer of</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">tophat considered the tool outdated. This affects the "singleended" test of bcbio, though.</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> -- Steffen Moeller Mon, 21 Jan 2019 21:30:11 +0100</span></pre>
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<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/bcbio/-/compare/cd8feac301800694e286f39f4104597b70d1d857...793c330de6805efac17fc4527d388778f5f52081#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</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">@@ -2,6 +2,8 @@ bcbio (1.2.8-1) UNRELEASED; urgency=medium</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> * New upstream version.</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * Standards-Version: 4.5.1 (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Removed now obsolete patch on abc collections</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Updated dependencies</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> -- Steffen Moeller <moeller@debian.org> Fri, 07 May 2021 20:29:57 +0200</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/bcbio/-/compare/cd8feac301800694e286f39f4104597b70d1d857...793c330de6805efac17fc4527d388778f5f52081#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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">@@ -27,6 +27,7 @@ Build-Depends: debhelper-compat (= 13),</td>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> bedtools <!nocheck>,</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"> biobambam2 <!nocheck>,</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"> bowtie2 <!nocheck>,</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> bwa <!nocheck>,</span>
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30
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31
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext"> cnvkit <!nocheck>,</span>
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31
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32
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext"> fastqc <!nocheck>,</span>
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32
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33
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"> freebayes <!nocheck>,</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="67" 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="68" 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">@@ -67,6 +68,7 @@ Build-Depends: debhelper-compat (= 13),</td>
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67
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68
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="plaintext"> samtools <!nocheck>,</span>
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68
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69
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="plaintext"> seqan-apps <!nocheck>,</span>
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69
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70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="plaintext"> seqtk <!nocheck>,</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext"> snpeff <!nocheck>,</span>
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70
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72
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="plaintext"> subread <!nocheck>,</span>
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71
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73
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="plaintext"> tabix <!nocheck>,</span>
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72
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="plaintext"> tophat-recondition <!nocheck>,</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="118" 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="120" 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">@@ -118,6 +120,7 @@ Recommends: cnvkit,</td>
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118
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120
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="plaintext"> r-bioc-purecn,</span>
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119
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121
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="plaintext"> r-bioc-titancna,</span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="plaintext"> seqan-apps,</span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext"> snpeff,</span>
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121
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="plaintext"> vcfanno,</span>
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122
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="plaintext"> vt</span>
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123
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="plaintext">Suggests: bcbio-doc,</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="142" 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="145" 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">@@ -142,6 +145,7 @@ Depends: ${python3:Depends},</td>
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142
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145
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="plaintext"> ${misc:Depends},</span>
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143
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146
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="plaintext"> python3-bcbio</span>
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144
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147
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="plaintext">Recommends: bcftools,</span>
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<td class="new_line diff-line-num new" data-linenumber="148" 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">
148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="plaintext"> bwa,</span>
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145
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149
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="plaintext"> cnvkit,</span>
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146
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150
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="plaintext"> cufflinks,</span>
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147
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151
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="plaintext"> delly,</span>
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<a href="https://salsa.debian.org/med-team/bcbio/-/compare/cd8feac301800694e286f39f4104597b70d1d857...793c330de6805efac17fc4527d388778f5f52081#0077a2c2838f7524dc36a2824fe4af986d35f032"><strong>debian/patches/collectionsAbc.patch</strong>
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<a href="https://salsa.debian.org/med-team/bcbio/-/compare/cd8feac301800694e286f39f4104597b70d1d857...793c330de6805efac17fc4527d388778f5f52081#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4" 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="4" 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">@@ -4,6 +4,5 @@ pytest2to3.patch</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">do_not_use_git.patch</span>
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<td class="old_line diff-line-num" 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">pythonpaths.patch</span>
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<td class="old_line diff-line-num" 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">hts_nim_tools.patch</span>
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<td class="old_line diff-line-num old" data-linenumber="7" 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="LC7" class="line" lang="plaintext">collectionsAbc.patch</span>
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<td class="old_line diff-line-num" data-linenumber="8" 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="new_line diff-line-num" data-linenumber="7" 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="LC7" class="line" lang="plaintext">cnvkitPath.patch</span>
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<td class="old_line diff-line-num" data-linenumber="9" 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="new_line diff-line-num" data-linenumber="8" 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="LC8" class="line" lang="plaintext">fixeFreetypePreload.patch</span></pre>
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