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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:
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<ul>
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<strong><a href="https://salsa.debian.org/med-team/python-pysam/commit/9a68cba764a0541c2ed7703ceed5a7f623a87d8f">9a68cba7</a></strong>
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<span>by Michael R. Crusoe</span>
<i>at 2020-01-02T15:27:17+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">sga already removed python2
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<strong><a href="https://salsa.debian.org/med-team/python-pysam/commit/52b5020d5ac19e63e1229d8406e75707bf41eec4">52b5020d</a></strong>
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<span>by Michael R. Crusoe</span>
<i>at 2020-01-03T21:27:27+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove hts_utell, no longer in libhts3
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<h4>3 changed files:</h4>
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<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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debian/patches/hts1.10
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<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/python-pysam/compare/f325a888db8cba2d4de66309c7d00ffd32f3b6a9...52b5020d5ac19e63e1229d8406e75707bf41eec4#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-1) <span class="idiff left right">UNRELEASED</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">python-pysam (0.15.3+ds-1) <span class="idiff left right">unstable</span>; urgency=medium</span>
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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"> * Team upload.</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> * New upstream release. Not yet dropping py2 due to paleomix<span class="idiff left right">, sga, others</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * New upstream release. Not yet dropping py2 due to paleomix<span class="idiff left right"> and pbsuite</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> * debhelper-compat 12</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> * Standards-Version: 4.4.0</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> * Trim trailing whitespace.</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> * Use secure URI in Homepage field.</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> * Set upstream metadata fields: Repository.</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> * New patch to remove symbols that were dropped in htslib 1.10:</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> hts_utell, hts_useek (Closes: #947426)</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> -- Michael R. Crusoe <michael.crusoe@gmail.com> <span class="idiff left right">Tue, 06 Aug 2019 19:37:44 +02</span>00</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> -- Michael R. Crusoe <michael.crusoe@gmail.com> <span class="idiff left right">Fri, 03 Jan 2020 21:25:33 +01</span>00</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">python-pysam (0.15.2+ds-2) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/python-pysam/compare/f325a888db8cba2d4de66309c7d00ffd32f3b6a9...52b5020d5ac19e63e1229d8406e75707bf41eec4#7a0b094a84dabf63ccc55c5b9d97b69a72a887f3"><strong>debian/patches/hts1.10</strong></a>
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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="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- python-pysam.orig/pysam/htslib_util.h</span></span>
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<pre style="margin: 0;">+<span id="LC4" 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="LC5" class="line" lang="diff"><span class="p">@@ -5,9 +5,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> #include "htslib/vcf.h"</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> #include "htslib/khash.h"</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-int hts_useek(htsFile *fp, long uoffset, int where);</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-long hts_utell(htsFile *fp);</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> int hts_set_verbosity(int verbosity);</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> int hts_get_verbosity(void);</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- python-pysam.orig/pysam/libchtslib.pxd</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ python-pysam/pysam/libchtslib.pxd</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="p">@@ -632,8 +632,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> int8_t HTS_FMT_CRAI</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> BGZF *hts_get_bgzfp(htsFile *fp)</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- int hts_useek(htsFile *fp, long uoffset, int where)</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- long hts_utell(htsFile *fp)</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> ctypedef struct hts_idx_t</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- python-pysam.orig/pysam/libchtslib.pyx</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ python-pysam/pysam/libchtslib.pyx</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="p">@@ -489,9 +489,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> if self.htsfile.format.compression == bgzf:</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> with nogil:</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> ret = bgzf_seek(hts_get_bgzfp(self.htsfile), offset, SEEK_SET)</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- elif self.htsfile.format.compression == no_compression:</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- with nogil:</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ret = hts_useek(self.htsfile, <int>offset, SEEK_SET)</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> else:</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> raise NotImplementedError("seek not implemented in files compressed by method {}".format(</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> self.htsfile.format.compression))</span>
</pre>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="p">@@ -508,9 +505,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> if self.htsfile.format.compression == bgzf:</span>
</pre>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> with nogil:</span>
</pre>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> ret = bgzf_tell(hts_get_bgzfp(self.htsfile))</span>
</pre>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- elif self.htsfile.format.compression == no_compression:</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="43" 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">
43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- with nogil:</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ret = hts_utell(self.htsfile)</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> elif self.htsfile.format.format == cram:</span>
</pre>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> with nogil:</span>
</pre>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> ret = htell(cram_fd_get_fp(self.htsfile.fp.cram))</span></pre>
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<a href="https://salsa.debian.org/med-team/python-pysam/compare/f325a888db8cba2d4de66309c7d00ffd32f3b6a9...52b5020d5ac19e63e1229d8406e75707bf41eec4#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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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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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">hts1.10</span></pre>
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