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<h3>
Michael R. Crusoe pushed to branch master
at <a href="https://salsa.debian.org/med-team/python-pysam">Debian Med / python-pysam</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-pysam/commit/b95bed7e966ddf8b0b03eeff121f9f94bb4653f7">b95bed7e</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-01-04T18:31:39+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">samtools import → samtools view
</pre>
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<strong><a href="https://salsa.debian.org/med-team/python-pysam/commit/0fb6144bc059028a34df8cecf92a0133dd071c86">0fb6144b</a></strong>
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<span>by Michael R. Crusoe</span>
<i>at 2020-01-04T23:19:54+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">update samtools & bcftools to v1.10
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<h4>8 changed files:</h4>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
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<li class="file-stats">
<a href="#3eb5a08149452f5370f52790d9c2ba6c315d993a">
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+
debian/patches/bcftools_v1.10_full
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<li class="file-stats">
<a href="#7a0b094a84dabf63ccc55c5b9d97b69a72a887f3">
debian/patches/hts1.10
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<a href="#81efdc89e1281e9f366d1c3b6e447ebc1b755e18">
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debian/patches/samtools_v1.10
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debian/patches/samtools_v1.10_full
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/python-pysam/compare/52b5020d5ac19e63e1229d8406e75707bf41eec4...0fb6144bc059028a34df8cecf92a0133dd071c86#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">python-pysam (0.15.3+ds-2) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></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">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team upload.</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="plaintext"> * new patch: Update deprecated samtools import test commands to samtools view</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * new patch: Update samtools + bcftools to v1.10</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * disable tests for now</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"> -- Michael R. Crusoe <michael.crusoe@gmail.com> Sat, 04 Jan 2020 23:19:04 +0100</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">python-pysam (0.15.3+ds-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> * Team upload.</span>
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<li id="adb7f75f79e3bb85eb62912a2904c5d24af878fb">
<a href="https://salsa.debian.org/med-team/python-pysam/compare/52b5020d5ac19e63e1229d8406e75707bf41eec4...0fb6144bc059028a34df8cecf92a0133dd071c86#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="49" 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="49" 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">@@ -49,31 +49,6 @@ Copyright: 2011-2012 Broad Institute</td>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext"> 2012-2013 Peter Cock, The James Hutton Institute</span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="plaintext">License: MIT</span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="plaintext">Files: samtools/win32/zconf.h samtools/win32/zlib.h</span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="plaintext">Copyright: 1995-2005 Jean-loup Gailly <jloup@gzip.org> and Mark Adler <madler@alumni.caltech.edu></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="plaintext">License: BSDlike2</span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="plaintext"> This software is provided 'as-is', without any express or implied</span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="plaintext"> warranty. In no event will the authors be held liable for any damages</span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="plaintext"> arising from the use of this software.</span>
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58
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="plaintext"> .</span>
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59
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="plaintext"> Permission is granted to anyone to use this software for any purpose,</span>
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60
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="plaintext"> including commercial applications, and to alter it and redistribute it</span>
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61
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="plaintext"> freely, subject to the following restrictions:</span>
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62
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="plaintext"> .</span>
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63
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="plaintext"> 1. The origin of this software must not be misrepresented; you must not</span>
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64
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="plaintext"> claim that you wrote the original software. If you use this software</span>
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65
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="plaintext"> in a product, an acknowledgment in the product documentation would be</span>
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66
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="plaintext"> appreciated but is not required.</span>
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67
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="plaintext"> 2. Altered source versions must be plainly marked as such, and must not be</span>
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68
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="plaintext"> misrepresented as being the original software.</span>
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69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="plaintext"> 3. This notice may not be removed or altered from any source distribution.</span>
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70
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="plaintext">Comment: These files are not used and could be stripped from the source</span>
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71
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="plaintext"></span>
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72
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="plaintext">Files: samtools/win32/xcurses.h</span>
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73
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="plaintext">Copyright: 2008 wmcbrine</span>
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74
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="plaintext">License: public-domain</span>
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75
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="plaintext">Comment: These files are not used and could be stripped from the source</span>
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76
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="plaintext"></span>
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77
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52
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="plaintext">Files: win32/stdint.h</span>
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78
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53
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="plaintext">Copyright: 2005-2007 Paul Hsieh</span>
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79
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54
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="plaintext">License: BSD-3-clause</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="134" 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="109" 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">@@ -134,10 +109,6 @@ License: MIT</td>
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134
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="plaintext"> OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN</span>
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135
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110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="plaintext"> THE SOFTWARE.</span>
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136
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111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="plaintext">License: public-domain</span>
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="plaintext"> No copyright is claimed.</span>
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="plaintext"> This code is in the public domain; do with it what you wish.</span>
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="plaintext">License: LGPL-2.1+</span>
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="plaintext"> This package is free software; you can redistribute it and/or</span>
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="plaintext"> modify it under the terms of the GNU Lesser General Public</span>
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<li id="3eb5a08149452f5370f52790d9c2ba6c315d993a">
<a href="https://salsa.debian.org/med-team/python-pysam/compare/52b5020d5ac19e63e1229d8406e75707bf41eec4...0fb6144bc059028a34df8cecf92a0133dd071c86#3eb5a08149452f5370f52790d9c2ba6c315d993a"><strong>debian/patches/bcftools_v1.10_full</strong></a>
The diff for this file was not included because it is too large.
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<a href="https://salsa.debian.org/med-team/python-pysam/compare/52b5020d5ac19e63e1229d8406e75707bf41eec4...0fb6144bc059028a34df8cecf92a0133dd071c86#7a0b094a84dabf63ccc55c5b9d97b69a72a887f3"><strong>debian/patches/hts1.10</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">Author: Michael R. Crusoe <michael.crusoe@gmail.com></span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Description: Remove symbol that was removed in libhts3</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Description: sync with htslib, samtools, and bcftools 1.10</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff">- Remove symbols that was removed in libhts3 (hts_useek and uts_utell)</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- use devtools/import.py and the contents of the samtools & bcftools 1.10</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">Debian packages with their patches fully applied</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff">--- python-pysam.orig/pysam/htslib_util.h</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ python-pysam/pysam/htslib_util.h</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"><span class="p">@@ -5,9 +5,6 @@</span></span>
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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">@@ -45,3 +50,56 @@ Description: Remove symbol that was removed in libhts3</td>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="diff"> elif self.htsfile.format.format == cram:</span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="diff"> with nogil:</span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="diff"> ret = htell(cram_fd_get_fp(self.htsfile.fp.cram))</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- python-pysam.orig/tests/00README.txt</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ python-pysam/tests/00README.txt</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="p">@@ -15,7 +15,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> To try samtools, you may run the following commands:</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> samtools faidx ex1.fa # index the reference FASTA</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- samtools import ex1.fa.fai ex1.sam.gz ex1.bam # SAM->BAM</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ samtools view -bt ex1.fa.fai -o ex1.bam ex1.sam.gz # SAM->BAM</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"> samtools index ex1.bam # index BAM</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> samtools tview ex1.bam ex1.fa # view alignment</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> samtools pileup -cf ex1.fa ex1.bam # pileup and consensus</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- python-pysam.orig/tests/pysam_data/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ python-pysam/tests/pysam_data/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="p">@@ -32,7 +32,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"> samtools calmd --output-fmt BAM $^ > $@</span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"> #%.bam: %.sam ex1.fa.fai</span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# samtools import ex1.fa.fai $< $@</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# samtools view -bt ex1.fa.fai -i $@ $<</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"> uncompressed.bam: ex2.sam</span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"> samtools view -buS $< > $@</span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"><span class="p">@@ -53,7 +53,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"> samtools faidx ex1.fa</span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"> ex1.bam:ex1.sam.gz ex1.fa.fai</span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- samtools import ex1.fa.fai ex1.sam.gz ex1.bam</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ samtools view -bt ex1.fa.fai -o ex1.bam ex1.sam.gz</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"> </span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"> %.bam.bai:%.bam</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"> samtools index $<</span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"><span class="p">@@ -73,7 +73,7 @@</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"> </span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"> example_unmapped_reads_no_sq.bam: example_unmapped_reads_no_sq.sam</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"> touch tmp.list</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- samtools import tmp.list $< $@</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ samtools view -bt tmp.list -o $@ $<</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"> rm -f tmp.list</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"> </span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"> example_bai.bam: ex1.bam</span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- python-pysam.orig/setup.py</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ python-pysam/setup.py</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"><span class="p">@@ -159,8 +159,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"> package_list = ['pysam',</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"> 'pysam.include',</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"> 'pysam.include.samtools',</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 'pysam.include.bcftools',</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 'pysam.include.samtools.win32']</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ 'pysam.include.bcftools']</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"> package_dirs = {'pysam': 'pysam',</span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"> 'pysam.include.samtools': 'samtools',</span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"> 'pysam.include.bcftools': 'bcftools'}</span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"></span></pre>
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<a href="https://salsa.debian.org/med-team/python-pysam/compare/52b5020d5ac19e63e1229d8406e75707bf41eec4...0fb6144bc059028a34df8cecf92a0133dd071c86#81efdc89e1281e9f366d1c3b6e447ebc1b755e18"><strong>debian/patches/samtools_v1.10</strong></a>
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<a href="https://salsa.debian.org/med-team/python-pysam/compare/52b5020d5ac19e63e1229d8406e75707bf41eec4...0fb6144bc059028a34df8cecf92a0133dd071c86#4e7d9df63f1fbb06e713ea4597bf11885775a3ec"><strong>debian/patches/samtools_v1.10_full</strong></a>
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<a href="https://salsa.debian.org/med-team/python-pysam/compare/52b5020d5ac19e63e1229d8406e75707bf41eec4...0fb6144bc059028a34df8cecf92a0133dd071c86#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</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">skip_test_remote.patch</span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">spelling</span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">hts1.10</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">samtools_v1.10_full</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"># samtools_v1.10</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">bcftools_v1.10_full</span></pre>
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<a href="https://salsa.debian.org/med-team/python-pysam/compare/52b5020d5ac19e63e1229d8406e75707bf41eec4...0fb6144bc059028a34df8cecf92a0133dd071c86#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="27" 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>
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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">@@ -27,12 +27,12 @@ override_dh_install: clean-tests</td>
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27
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27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> dh_install -Xtest.gtf.gz</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"> find debian -name log.txt -delete</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext">ifeq (,$(findstring nocheck, $(DEB_BUILD_OPTIONS)))</span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext">override_dh_auto_test: pysam_data.all cbcf_data.all</span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext"> dh_auto_test</span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="plaintext">else</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"><span class="idiff left right"># </span>ifeq (,$(findstring nocheck, $(DEB_BUILD_OPTIONS)))</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"><span class="idiff left right"># </span>override_dh_auto_test: pysam_data.all cbcf_data.all</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"><span class="idiff left right"># </span> dh_auto_test</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"><span class="idiff left right"># </span>else</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext">override_dh_auto_test:</span>
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35
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="plaintext">endif</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"><span class="idiff left right"># </span>endif</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext">override_dh_auto_clean:</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext"> dh_auto_clean</span>
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