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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/minimap2">Debian Med / minimap2</a>
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<h4>
Commits:
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<ul>
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<strong><a href="https://salsa.debian.org/med-team/minimap2/-/commit/1cc6340dc29294003aed025f235e97942bcc6fa7">1cc6340d</a></strong>
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<span>by Andreas Tille</span>
<i>at 2020-05-13T12:58:10+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Provide Python3 interface
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<strong><a href="https://salsa.debian.org/med-team/minimap2/-/commit/bc4e160c7e75cd43a0c2e9b6e149006e76df22a8">bc4e160c</a></strong>
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<span>by Andreas Tille</span>
<i>at 2020-05-13T13:16:29+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">TODO: Fix simde linking
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<h4>4 changed files:</h4>
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<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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+
debian/python3-mappy.install
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/minimap2/-/compare/8976720d09bd3f17167d5433594a9f10e17d4f45...bc4e160c7e75cd43a0c2e9b6e149006e76df22a8#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">minimap2 (2.17+dfsg-10) UNRELEASED; 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"> * Provide Python3 interface</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> TODO: Fix simde linking:</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> >>> import mappy</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> Traceback (most recent call last):</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> File "<stdin>", line 1, in <module></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> ImportError: /usr/lib/python3/dist-packages/mappy.cpython-38-x86_64-linux-gnu.so: undefined symbol: ksw_extz2_sse</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"> -- Andreas Tille <tille@debian.org> Wed, 13 May 2020 11:44:53 +0200</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">minimap2 (2.17+dfsg-9) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> * Team upload.</span>
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<a href="https://salsa.debian.org/med-team/minimap2/-/compare/8976720d09bd3f17167d5433594a9f10e17d4f45...bc4e160c7e75cd43a0c2e9b6e149006e76df22a8#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">@@ -4,6 +4,9 @@ Uploaders: Andreas Tille <tille@debian.org></td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 12),</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> dh-python,</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> cython3,</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> python3-all-dev,</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> d-shlibs,</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> zlib1g-dev,</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> texlive-latex-extra,</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">@@ -61,3 +64,22 @@ Description: development headers for libminimap</td>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="plaintext"> This package contains the C library headers for using minimap in custom tools,</span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="plaintext"> along with a static library.</span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">Package: python3-mappy</span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext">Architecture: any</span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">Section: python</span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext"> ${python3:Depends},</span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext"> ${misc:Depends}</span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext">Description: Python3 interface minimap2</span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext"> Minimap2 is a versatile sequence alignment program that aligns DNA or</span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext"> mRNA sequences against a large reference database. Typical use cases</span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext"> include: (1) mapping PacBio or Oxford Nanopore genomic reads to the</span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext"> human genome; (2) finding overlaps between long reads with error rate up</span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext"> to ~15%; (3) splice-aware alignment of PacBio Iso-Seq or Nanopore cDNA</span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext"> or Direct RNA reads against a reference genome; (4) aligning Illumina</span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext"> single- or paired-end reads; (5) assembly-to-assembly alignment; (6) full-</span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext"> genome alignment between two closely related species with divergence</span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext"> below ~15%.</span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext"> This package contains the Python3 interface for using minimap2.</span></pre>
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<li id="7e46c9565511899b0d3143135bb944daf1fd980c">
<a href="https://salsa.debian.org/med-team/minimap2/-/compare/8976720d09bd3f17167d5433594a9f10e17d4f45...bc4e160c7e75cd43a0c2e9b6e149006e76df22a8#7e46c9565511899b0d3143135bb944daf1fd980c"><strong>debian/python3-mappy.install</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="o" style="font-weight: 600;">/</span><span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">lib</span><span class="o" style="font-weight: 600;">/</span><span class="nx">python3</span><span class="o" style="font-weight: 600;">*</span></span></pre>
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<a href="https://salsa.debian.org/med-team/minimap2/-/compare/8976720d09bd3f17167d5433594a9f10e17d4f45...bc4e160c7e75cd43a0c2e9b6e149006e76df22a8#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</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">@@ -9,7 +9,7 @@ export DEB_CFLAGS_MAINT_APPEND += -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">RANLIB ?= ranlib</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">%:</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> dh $@</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> dh $@<span class="idiff left right"> --with python3</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">override_dh_auto_clean:</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> dh_auto_clean</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">@@ -26,6 +26,7 @@ endif</td>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">override_dh_auto_build:</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> dh_auto_build -- $(build_vars)</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"> cd tex && make</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> dh_auto_build --buildsystem=pybuild</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext">override_dh_auto_test:</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext">ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -33,6 +34,10 @@ ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</td>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"> rm test.sam</span>
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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="LC36" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">override_dh_auto_install:</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"> dh_auto_install</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"> dh_auto_install --buildsystem=pybuild</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext">override_dh_compress:</span>
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<td class="diff-line-num old_line" data-linenumber="37" 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">
37
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42
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext"> dh_compress --exclude=.pdf</span>
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<td class="diff-line-num old_line" data-linenumber="38" 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">
38
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43
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext"></span>
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