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<h3>
Nilesh Patra pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/python-ncls">Debian Med / python-ncls</a>
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<h4>
Commits:
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<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-ncls/-/commit/bc53e2626eb2f1fa60f2e94db42b5603dc5ed21f">bc53e262</a></strong>
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<span>by Nilesh Patra</span>
<i>at 2020-10-13T11:57:45+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.0.56+ds</pre>
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<h4>8 changed files:</h4>
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<li class="file-stats">
<a href="#1c497fbb3a46b78edf04cc2a2fa33f67e3ffbe2a">
CHANGELOG
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<li class="file-stats">
<a href="#bb16a23e0e5b95e20237af5b7bd488cf49c22509">
ncls/src/cncls.pxd
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<li class="file-stats">
<a href="#8f6f5e57bce6cb28590d6273e93f5eefc91f8c35">
ncls/src/intervaldb.c
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<li class="file-stats">
<a href="#3c610847736e1cc195a7b4b74ffe5f928c84ab41">
ncls/src/intervaldb.h
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<li class="file-stats">
<a href="#9f5513a7b12c629ad6d3563e589e4ea34bfd934e">
ncls/src/ncls.pyx
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<li class="file-stats">
<a href="#2472d5ab835e981576a859a20c8c459d3654e4c0">
ncls/version.py
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<li class="file-stats">
<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
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<li class="file-stats">
<a href="#9b92cd32e2b5df39b01e80658cc548f69af39e6a">
tests/test_ncls.py
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<h4>Changes:</h4>
<li id="1c497fbb3a46b78edf04cc2a2fa33f67e3ffbe2a">
<a href="https://salsa.debian.org/med-team/python-ncls/-/commit/bc53e2626eb2f1fa60f2e94db42b5603dc5ed21f#1c497fbb3a46b78edf04cc2a2fa33f67e3ffbe2a"><strong>CHANGELOG</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext"># 0.0.53 (unreleased)</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"># 0.0.55-56 (12.10.20)</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">- fix build on 32-bit architectures (thanks to nileshpatra)</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"># 0.0.54 (14.09.20)</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">- fix #38 (thanks fireice-uk)</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"># 0.0.53 (?)</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">- add datastructure FNCLS which uses floating point starts and ends</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"># 0.0.52 (20.02.20)</span>
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<a href="https://salsa.debian.org/med-team/python-ncls/-/commit/bc53e2626eb2f1fa60f2e94db42b5603dc5ed21f#bb16a23e0e5b95e20237af5b7bd488cf49c22509"><strong>ncls/src/cncls.pxd</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">@@ -52,8 +52,8 @@ cdef extern from "ncls/src/intervaldb.h":</td>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="cython"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">start</span></span>
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53
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="cython"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nb" style="color: #0086b3;">len</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="cython"></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="cython"> <span class="nb" style="color: #0086b3;">int</span> <span class="nf" style="color: #900; font-weight: 600;">find_overlap_start</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">IntervalMap</span> <span class="n" style="color: #333;">im</span><span class="p">[],</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="cython"> <span class="nb" style="color: #0086b3;">int</span> <span class="nf" style="color: #900; font-weight: 600;">find_suboverlap_start</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">isub</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">IntervalMap</span> <span class="n" style="color: #333;">im</span><span class="p">[],</span> <span class="kt" style="color: #458; font-weight: 600;">SublistHeader</span> <span class="n" style="color: #333;">subheader</span><span class="p">[])</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="cython"> <span class="n" style="color: #333;">int<span class="idiff left right">64_t</span></span> <span class="nf" style="color: #900; font-weight: 600;">find_overlap_start</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">IntervalMap</span> <span class="n" style="color: #333;">im</span><span class="p">[],</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="cython"> <span class="n" style="color: #333;">int<span class="idiff left right">64_t</span></span> <span class="nf" style="color: #900; font-weight: 600;">find_suboverlap_start</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">isub</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">IntervalMap</span> <span class="n" style="color: #333;">im</span><span class="p">[],</span> <span class="kt" style="color: #458; font-weight: 600;">SublistHeader</span> <span class="n" style="color: #333;">subheader</span><span class="p">[])</span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="cython"> <span class="nb" style="color: #0086b3;">int</span> <span class="nf" style="color: #900; font-weight: 600;">imstart_qsort_cmp</span><span class="p">(</span><span class="n" style="color: #333;">void</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">void_a</span><span class="p">,</span><span class="n" style="color: #333;">void</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">void_b</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="cython"> <span class="n" style="color: #333;">IntervalMap</span> <span class="o" style="font-weight: 600;">*</span><span class="nf" style="color: #900; font-weight: 600;">read_intervals</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span><span class="p">,</span><span class="n" style="color: #333;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ifile</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="cython"> <span class="n" style="color: #333;">SublistHeader</span> <span class="o" style="font-weight: 600;">*</span><span class="nf" style="color: #900; font-weight: 600;">build_nested_list</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">IntervalMap</span> <span class="n" style="color: #333;">im</span><span class="p">[],</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span><span class="p">,</span><span class="nb" style="color: #0086b3;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">p_n</span><span class="p">,</span><span class="nb" style="color: #0086b3;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">p_nlists</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/python-ncls/-/commit/bc53e2626eb2f1fa60f2e94db42b5603dc5ed21f#8f6f5e57bce6cb28590d6273e93f5eefc91f8c35"><strong>ncls/src/intervaldb.c</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">@@ -370,10 +370,10 @@ int find_index_start(int start,int end,IntervalIndex im[],int n)</td>
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<pre style="margin: 0;"> <span id="LC372" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC373" class="line" lang="c"><span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="idiff left"> </span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff">find_suboverlap_start</span></span><span class="p"><span class="idiff">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">start</span></span><span class="p"><span class="idiff">,</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">end</span></span><span class="p"><span class="idiff">,</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">isub</span></span><span class="p"><span class="idiff right">,</span></span><span class="n" style="color: #333;">IntervalMap</span> <span class="n" style="color: #333;">im</span><span class="p">[],</span></span>
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="c"><span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">int<span class="idiff left">64_t</span></span><span class="idiff"> </span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff">find_suboverlap_start</span></span><span class="p"><span class="idiff">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int64_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">start</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int64_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">end</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">isub</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">IntervalMap</span> <span class="n" style="color: #333;">im</span><span class="p">[],</span></span>
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<pre style="margin: 0;"> <span id="LC374" class="line" lang="c"> <span class="n" style="color: #333;">SublistHeader</span> <span class="n" style="color: #333;">subheader</span><span class="p">[])</span></span>
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<pre style="margin: 0;"> <span id="LC375" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC376" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int<span class="idiff left right">64_t</span></span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC377" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC378" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isub</span><span class="o" style="font-weight: 600;">>=</span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC379" class="line" lang="c"> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">find_overlap_start</span><span class="p">(</span><span class="n" style="color: #333;">start</span><span class="p">,</span><span class="n" style="color: #333;">end</span><span class="p">,</span><span class="n" style="color: #333;">im</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">subheader</span><span class="p">[</span><span class="n" style="color: #333;">isub</span><span class="p">].</span><span class="n" style="color: #333;">start</span><span class="p">,</span><span class="n" style="color: #333;">subheader</span><span class="p">[</span><span class="n" style="color: #333;">isub</span><span class="p">].</span><span class="n" style="color: #333;">len</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/python-ncls/-/commit/bc53e2626eb2f1fa60f2e94db42b5603dc5ed21f#3c610847736e1cc195a7b4b74ffe5f928c84ab41"><strong>ncls/src/intervaldb.h</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">@@ -77,8 +77,8 @@ typedef struct {</td>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="nf" style="color: #900; font-weight: 600;">alloc_array</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="nf" style="color: #900; font-weight: 600;">find_overlap_start</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">start</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">int64_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">end</span></span><span class="p"><span class="idiff right">,</span></span><span class="n" style="color: #333;">IntervalMap</span> <span class="n" style="color: #333;">im</span><span class="p">[],</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="idiff left"> </span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff">find_suboverlap_start</span></span><span class="p"><span class="idiff">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">start</span></span><span class="p"><span class="idiff">,</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">end</span></span><span class="p"><span class="idiff">,</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">isub</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">IntervalMap</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">im</span></span><span class="p"><span class="idiff right">[],</span></span><span class="n" style="color: #333;">SublistHeader</span> <span class="n" style="color: #333;">subheader</span><span class="p">[]);</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="nf" style="color: #900; font-weight: 600;">find_overlap_start</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">start</span><span class="p">,</span><span class="idiff left"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int64_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">end</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">IntervalMap</span> <span class="n" style="color: #333;">im</span><span class="p">[],</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">int<span class="idiff left">64_t</span></span><span class="idiff"> </span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff">find_suboverlap_start</span></span><span class="p"><span class="idiff">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int64_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">start</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int64_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">end</span></span><span class="p"><span class="idiff">,</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">isub</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">IntervalMap</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">im</span></span><span class="p"><span class="idiff">[],</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">SublistHeader</span> <span class="n" style="color: #333;">subheader</span><span class="p">[]);</span></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">imstart_qsort_cmp</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">void_a</span><span class="p">,</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">void_b</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">target_qsort_cmp</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">void_a</span><span class="p">,</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">void_b</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="n" style="color: #333;">IntervalMap</span> <span class="o" style="font-weight: 600;">*</span><span class="nf" style="color: #900; font-weight: 600;">read_intervals</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ifile</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/python-ncls/-/commit/bc53e2626eb2f1fa60f2e94db42b5603dc5ed21f#9f5513a7b12c629ad6d3563e589e4ea34bfd934e"><strong>ncls/src/ncls.pyx</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">@@ -150,7 +150,7 @@ cdef class NCLS64:</td>
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="cython"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">cython</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">boundscheck</span><span class="p">(</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="cython"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">cython</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">wraparound</span><span class="p">(</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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152
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152
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="cython"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">cython</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">initializedcheck</span><span class="p">(</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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153
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cpdef</span> <span class="nf" style="color: #900; font-weight: 600;">last_overlap_both</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">const</span> <span class="n" style="color: #333;">int64_t</span> <span class="p">[::</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="n" style="color: #333;">starts</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">const</span> <span class="n" style="color: #333;">int64_t</span> <span class="p">[::</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="n" style="color: #333;">ends</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">const</span> <span class="nb" style="color: #0086b3;"><span class="idiff left right">long</span></span> <span class="p">[::</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="n" style="color: #333;">indexes</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cpdef</span> <span class="nf" style="color: #900; font-weight: 600;">last_overlap_both</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">const</span> <span class="n" style="color: #333;">int64_t</span> <span class="p">[::</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="n" style="color: #333;">starts</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">const</span> <span class="n" style="color: #333;">int64_t</span> <span class="p">[::</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="n" style="color: #333;">ends</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">const</span> <span class="n" style="color: #333;"><span class="idiff left right">int64_t</span></span> <span class="p">[::</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="n" style="color: #333;">indexes</span><span class="p">):</span></span>
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154
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="cython"></span>
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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156
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156
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nhit</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="159" 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">@@ -159,10 +159,10 @@ cdef class NCLS64:</td>
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159
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159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nfound</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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160
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160
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">max_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span></span>
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161
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161
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="cython"></span>
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162
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="cython"> <span class="n" style="color: #333;">output_arr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">zeros</span><span class="p">(</span><span class="n" style="color: #333;">length</span><span class="p">,</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;"><span class="idiff left right">long</span></span><span class="p">)</span></span>
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163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="cython"> <span class="n" style="color: #333;">output_arr_other</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">zeros</span><span class="p">(</span><span class="n" style="color: #333;">length</span><span class="p">,</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;"><span class="idiff left right">long</span></span><span class="p">)</span></span>
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164
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">long</span></span> <span class="p">[::</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="n" style="color: #333;">output</span></span>
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165
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">long</span></span> <span class="p">[::</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="n" style="color: #333;">output_other</span></span>
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="cython"> <span class="n" style="color: #333;">output_arr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">zeros</span><span class="p">(</span><span class="n" style="color: #333;">length</span><span class="p">,</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;"><span class="idiff left">np</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">int64</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="cython"> <span class="n" style="color: #333;">output_arr_other</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">zeros</span><span class="p">(</span><span class="n" style="color: #333;">length</span><span class="p">,</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;"><span class="idiff left">np</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">int64</span></span><span class="p">)</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">int64_t</span></span> <span class="p">[::</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="n" style="color: #333;">output</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">int64_t</span></span> <span class="p">[::</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="n" style="color: #333;">output_other</span></span>
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166
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="cython"></span>
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="cython"> <span class="n" style="color: #333;">output</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">output_arr</span></span>
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168
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168
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="cython"> <span class="n" style="color: #333;">output_other</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">output_arr_other</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">@@ -588,8 +588,8 @@ cdef class NCLS64:</td>
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<pre style="margin: 0;"> <span id="LC588" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">loop_counter</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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589
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<pre style="margin: 0;"> <span id="LC589" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nfound</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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590
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<pre style="margin: 0;"> <span id="LC590" class="line" lang="cython"></span>
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<pre style="margin: 0;">-<span id="LC591" class="line" lang="cython"> <span class="n" style="color: #333;">output_arr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">zeros</span><span class="p">(</span><span class="n" style="color: #333;">length</span><span class="p">,</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nb" style="color: #0086b3;"><span class="idiff left right">long</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC592" class="line" lang="cython"> <span class="n" style="color: #333;">output_arr_other</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">zeros</span><span class="p">(</span><span class="n" style="color: #333;">length</span><span class="p">,</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nb" style="color: #0086b3;"><span class="idiff left right">long</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC591" class="line" lang="cython"> <span class="n" style="color: #333;">output_arr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">zeros</span><span class="p">(</span><span class="n" style="color: #333;">length</span><span class="p">,</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">int64</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC592" class="line" lang="cython"> <span class="n" style="color: #333;">output_arr_other</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">zeros</span><span class="p">(</span><span class="n" style="color: #333;">length</span><span class="p">,</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">int64</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC593" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="p">[::</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="n" style="color: #333;">output</span></span>
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594
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<pre style="margin: 0;"> <span id="LC594" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="p">[::</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="n" style="color: #333;">output_other</span></span>
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<pre style="margin: 0;"> <span id="LC595" class="line" lang="cython"></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">@@ -630,8 +630,8 @@ cdef class NCLS64:</td>
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<pre style="margin: 0;"> <span id="LC630" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nfound</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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631
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631
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<pre style="margin: 0;"> <span id="LC631" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">end</span></span>
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<pre style="margin: 0;"> <span id="LC632" class="line" lang="cython"></span>
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<pre style="margin: 0;">-<span id="LC633" class="line" lang="cython"> <span class="n" style="color: #333;">output_arr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">zeros</span><span class="p">(</span><span class="n" style="color: #333;">length</span><span class="p">,</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nb" style="color: #0086b3;"><span class="idiff left right">long</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC634" class="line" lang="cython"> <span class="n" style="color: #333;">output_arr_other</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">zeros</span><span class="p">(</span><span class="n" style="color: #333;">length</span><span class="p">,</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nb" style="color: #0086b3;"><span class="idiff left right">long</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC633" class="line" lang="cython"> <span class="n" style="color: #333;">output_arr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">zeros</span><span class="p">(</span><span class="n" style="color: #333;">length</span><span class="p">,</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">int64</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC634" class="line" lang="cython"> <span class="n" style="color: #333;">output_arr_other</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">zeros</span><span class="p">(</span><span class="n" style="color: #333;">length</span><span class="p">,</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">int64</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC635" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="p">[::</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="n" style="color: #333;">output</span></span>
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<pre style="margin: 0;"> <span id="LC636" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="p">[::</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="n" style="color: #333;">output_other</span></span>
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<pre style="margin: 0;"> <span id="LC637" class="line" lang="cython"></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">@@ -725,10 +725,10 @@ cdef class NCLSIterator:</td>
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<pre style="margin: 0;"> <span id="LC725" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="n" style="color: #333;">cn</span><span class="p">.</span><span class="n" style="color: #333;">IntervalIterator</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">it_alloc</span></span>
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726
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<pre style="margin: 0;"> <span id="LC726" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="n" style="color: #333;">cn</span><span class="p">.</span><span class="n" style="color: #333;">IntervalMap</span> <span class="n" style="color: #333;">im_buf</span><span class="p">[</span><span class="mi" style="color: #099;">1024</span><span class="p">]</span></span>
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727
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<pre style="margin: 0;"> <span id="LC727" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nhit</span><span class="p">,</span> <span class="n" style="color: #333;">ihit</span></span>
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<pre style="margin: 0;">-<span id="LC728" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC728" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">end</span></span>
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<pre style="margin: 0;"> <span id="LC729" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">NCLS64</span> <span class="n" style="color: #333;">db</span></span>
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<pre style="margin: 0;"> <span id="LC730" class="line" lang="cython"></span>
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<pre style="margin: 0;">-<span id="LC731" class="line" lang="cython"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__cinit__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">long</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">start</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff right">long</span></span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">NCLS64</span> <span class="n" style="color: #333;">db</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC731" class="line" lang="cython"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__cinit__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">int64_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">start</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff right">int64_t</span></span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">NCLS64</span> <span class="n" style="color: #333;">db</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC732" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cn</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">interval_iterator_alloc</span><span class="p">()</span></span>
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733
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<pre style="margin: 0;"> <span id="LC733" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">it_alloc</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">it</span></span>
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734
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734
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<pre style="margin: 0;"> <span id="LC734" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">start</span></span>
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<a href="https://salsa.debian.org/med-team/python-ncls/-/commit/bc53e2626eb2f1fa60f2e94db42b5603dc5ed21f#2472d5ab835e981576a859a20c8c459d3654e4c0"><strong>ncls/version.py</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0.0.5<span class="idiff left right">3</span>"</span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0.0.5<span class="idiff left right">6</span>"</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-ncls/-/commit/bc53e2626eb2f1fa60f2e94db42b5603dc5ed21f#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.py</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">distutils.core</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">setup</span></span>
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2
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">setuptools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">find_packages</span><span class="p">,</span> <span class="n" style="color: #333;">Extension</span><span class="p">,</span> <span class="n" style="color: #333;">Command</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">distutils.core</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">setup</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># try:</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">@@ -94,4 +94,3 @@ setup(</td>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="python"> <span class="n" style="color: #333;">package_data</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span><span class="s" style="color: #d14;">''</span><span class="p">:</span> <span class="p">[</span><span class="s" style="color: #d14;">'*.pyx'</span><span class="p">,</span> <span class="s" style="color: #d14;">'*.pxd'</span><span class="p">,</span> <span class="s" style="color: #d14;">'*.h'</span><span class="p">,</span> <span class="s" style="color: #d14;">'*.c'</span><span class="p">]},</span></span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="python"> <span class="n" style="color: #333;">include_dirs</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">"."</span><span class="p">],</span></span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="python"><span class="p">)</span></span></pre>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="python"></span></pre>
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<a href="https://salsa.debian.org/med-team/python-ncls/-/commit/bc53e2626eb2f1fa60f2e94db42b5603dc5ed21f#9b92cd32e2b5df39b01e80658cc548f69af39e6a"><strong>tests/test_ncls.py</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">struct</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">ncls</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">NCLS</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">numpy</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">np</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="python"><span class="n" style="color: #333;">starts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">([</span><span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="mi" style="color: #099;">9_223_372_036_854_775_805</span><span class="p">],</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nb" style="color: #0086b3;">long</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="python"><span class="n" style="color: #333;">ends</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">([</span><span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="mi" style="color: #099;">9_223_372_036_854_775_807</span><span class="p">],</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nb" style="color: #0086b3;">long</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">struct</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># 64 bit architecture?</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">struct</span><span class="p">.</span><span class="n" style="color: #333;">calcsize</span><span class="p">(</span><span class="s" style="color: #d14;">"P"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">8</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">64</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="python"><span class="n" style="color: #333;"><span class="idiff left">ids</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">np</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">array</span></span><span class="p"><span class="idiff">([</span></span><span class="mi" style="color: #099;"><span class="idiff">2147483647</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">3</span></span><span class="p"><span class="idiff">],</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">dtype</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">np</span></span><span class="p"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff right">long</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">starts</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">np</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">array</span></span><span class="p"><span class="idiff">([</span></span><span class="mi" style="color: #099;"><span class="idiff">5</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">9_223_372_036_854_775_805</span></span><span class="p"><span class="idiff">],</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">dtype</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">np</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">int64</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_ncls</span><span class="p">():</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># ids = starts</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"> <span class="n" style="color: #333;">ends</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">([</span><span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="mi" style="color: #099;">9_223_372_036_854_775_807</span><span class="p">],</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">int64</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left">print</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">starts</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ends</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">ids</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">ids</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">np</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">array</span></span><span class="p"><span class="idiff">([</span></span><span class="mi" style="color: #099;"><span class="idiff">2147483647</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">3</span></span><span class="p"><span class="idiff">],</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">dtype</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">np</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">int64</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="python"> <span class="n" style="color: #333;">ncls</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NCLS</span><span class="p">(</span><span class="n" style="color: #333;">starts</span><span class="p">,</span> <span class="n" style="color: #333;">ends</span><span class="p">,</span> <span class="n" style="color: #333;">ids</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">ncls</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">ncls</span><span class="p">.</span><span class="n" style="color: #333;">intervals</span><span class="p">())</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_ncls</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># ids = starts</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">ncls</span><span class="p">.</span><span class="n" style="color: #333;">find_overlap</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">))</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"aaa"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">ncls</span><span class="p">.</span><span class="n" style="color: #333;">find_overlap</span><span class="p">(</span><span class="mi" style="color: #099;">9_223_372_036_854_775_805</span><span class="p">,</span> <span class="mi" style="color: #099;">9_223_372_036_854_775_806</span><span class="p">)))</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">ncls</span><span class="p">.</span><span class="n" style="color: #333;">find_overlap</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">9_223_372_036_854_775_806</span><span class="p">))</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[(</span><span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="mi" style="color: #099;">2147483647</span><span class="p">),</span> <span class="p">(</span><span class="mi" style="color: #099;">9223372036854775805</span><span class="p">,</span> <span class="mi" style="color: #099;">9223372036854775807</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">)]</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">starts</span><span class="p">,</span> <span class="n" style="color: #333;">ends</span><span class="p">,</span> <span class="n" style="color: #333;">ids</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">r</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">l</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ncls</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">all_overlaps_both</span></span><span class="p">(</span><span class="n" style="color: #333;">starts</span><span class="p">,</span> <span class="n" style="color: #333;">ends</span><span class="p">,</span> <span class="n" style="color: #333;">ids</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left">assert</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">list</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">r</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">2147483647</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">3</span></span><span class="p"><span class="idiff right">]</span></span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left">assert</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">list</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">l</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">2147483647</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">3</span></span><span class="p"><span class="idiff right">]</span></span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">ncls</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">NCLS</span></span><span class="p">(</span><span class="n" style="color: #333;">starts</span><span class="p">,</span> <span class="n" style="color: #333;">ends</span><span class="p">,</span> <span class="n" style="color: #333;">ids</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">print</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">ncls</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">print</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">ncls</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">intervals</span></span><span class="p"><span class="idiff right">())</span></span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_all_containments_both</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">ncls</span><span class="p">.</span><span class="n" style="color: #333;">find_overlap</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">))</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"aaa"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">ncls</span><span class="p">.</span><span class="n" style="color: #333;">find_overlap</span><span class="p">(</span><span class="mi" style="color: #099;">9_223_372_036_854_775_805</span><span class="p">,</span> <span class="mi" style="color: #099;">9_223_372_036_854_775_806</span><span class="p">)))</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">ncls</span><span class="p">.</span><span class="n" style="color: #333;">find_overlap</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">9_223_372_036_854_775_806</span><span class="p">))</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[(</span><span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="mi" style="color: #099;">2147483647</span><span class="p">),</span> <span class="p">(</span><span class="mi" style="color: #099;">9223372036854775805</span><span class="p">,</span> <span class="mi" style="color: #099;">9223372036854775807</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">)]</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">starts</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">np</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">array</span></span><span class="p"><span class="idiff">([</span></span><span class="mi" style="color: #099;"><span class="idiff">1291845632</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">3002335232</span></span><span class="p"><span class="idiff">],</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">dtype</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="nb" style="color: #0086b3;"><span class="idiff right">int</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">ends</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">np</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">array</span></span><span class="p"><span class="idiff">([</span></span><span class="mi" style="color: #099;"><span class="idiff">1292894207</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">3002597375</span></span><span class="p"><span class="idiff">],</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">dtype</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">int</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">ids</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">np</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">array</span></span><span class="p"><span class="idiff">([</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">],</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">dtype</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">int</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">r</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">l</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ncls</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">all_overlaps_both</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">starts</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ends</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">ids</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">assert</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">list</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">r</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">2147483647</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">3</span></span><span class="p"><span class="idiff right">]</span></span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"> <span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">assert</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">list</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">l</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">2147483647</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">3</span></span><span class="p"><span class="idiff right">]</span></span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="python"> <span class="n" style="color: #333;">ncls</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NCLS</span><span class="p">(</span><span class="n" style="color: #333;">starts</span><span class="p">,</span> <span class="n" style="color: #333;">ends</span><span class="p">,</span> <span class="n" style="color: #333;">ids</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="python"> <span class="n" style="color: #333;">subs</span><span class="p">,</span> <span class="n" style="color: #333;">covers</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ncls</span><span class="p">.</span><span class="n" style="color: #333;">all_containments_both</span><span class="p">(</span><span class="n" style="color: #333;">starts</span><span class="p">,</span> <span class="n" style="color: #333;">ends</span><span class="p">,</span> <span class="n" style="color: #333;">ids</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_all_containments_both</span><span class="p">():</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">ncls</span><span class="p">.</span><span class="n" style="color: #333;">intervals</span><span class="p">())</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"> <span class="n" style="color: #333;">starts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">([</span><span class="mi" style="color: #099;">1291845632</span><span class="p">,</span> <span class="mi" style="color: #099;">3002335232</span><span class="p">],</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">int64</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="n" style="color: #333;">ends</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">([</span><span class="mi" style="color: #099;">1292894207</span><span class="p">,</span> <span class="mi" style="color: #099;">3002597375</span><span class="p">],</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">int64</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="n" style="color: #333;">ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">([</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">int64</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">subs</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">covers</span><span class="p">)</span></span></pre>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"> <span class="n" style="color: #333;">ncls</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NCLS</span><span class="p">(</span><span class="n" style="color: #333;">starts</span><span class="p">,</span> <span class="n" style="color: #333;">ends</span><span class="p">,</span> <span class="n" style="color: #333;">ids</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> <span class="n" style="color: #333;">subs</span><span class="p">,</span> <span class="n" style="color: #333;">covers</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ncls</span><span class="p">.</span><span class="n" style="color: #333;">all_containments_both</span><span class="p">(</span><span class="n" style="color: #333;">starts</span><span class="p">,</span> <span class="n" style="color: #333;">ends</span><span class="p">,</span> <span class="n" style="color: #333;">ids</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">ncls</span><span class="p">.</span><span class="n" style="color: #333;">intervals</span><span class="p">())</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">subs</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">covers</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"><span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="n" style="color: #333;">starts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">([</span><span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="mi" style="color: #099;">2_147_483_645</span><span class="p">],</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">int64</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="n" style="color: #333;">ends</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">([</span><span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="mi" style="color: #099;">2_147_483_646</span><span class="p">],</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">int64</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="n" style="color: #333;">ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">([</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">],</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">int64</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_ncls</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># ids = starts</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">starts</span><span class="p">,</span> <span class="n" style="color: #333;">ends</span><span class="p">,</span> <span class="n" style="color: #333;">ids</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"> <span class="n" style="color: #333;">ncls</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NCLS</span><span class="p">(</span><span class="n" style="color: #333;">starts</span><span class="p">,</span> <span class="n" style="color: #333;">ends</span><span class="p">,</span> <span class="n" style="color: #333;">ids</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">ncls</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">ncls</span><span class="p">.</span><span class="n" style="color: #333;">intervals</span><span class="p">())</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">ncls</span><span class="p">.</span><span class="n" style="color: #333;">find_overlap</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">))</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">ncls</span><span class="p">.</span><span class="n" style="color: #333;">find_overlap</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">2_147_483_647</span><span class="p">))</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[(</span><span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="p">(</span><span class="mi" style="color: #099;">2_147_483_645</span><span class="p">,</span> <span class="mi" style="color: #099;">2_147_483_646</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">)]</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"> <span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ncls</span><span class="p">.</span><span class="n" style="color: #333;">all_overlaps_both</span><span class="p">(</span><span class="n" style="color: #333;">starts</span><span class="p">,</span> <span class="n" style="color: #333;">ends</span><span class="p">,</span> <span class="n" style="color: #333;">ids</span><span class="p">)</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">]</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">]</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_all_containments_both</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"> <span class="n" style="color: #333;">starts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">([</span><span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">],</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">int64</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"> <span class="n" style="color: #333;">ends</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">([</span><span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="mi" style="color: #099;">50</span><span class="p">],</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">int64</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"> <span class="n" style="color: #333;">ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">([</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">int64</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"> <span class="n" style="color: #333;">ncls</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NCLS</span><span class="p">(</span><span class="n" style="color: #333;">starts</span><span class="p">,</span> <span class="n" style="color: #333;">ends</span><span class="p">,</span> <span class="n" style="color: #333;">ids</span><span class="p">)</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"> <span class="n" style="color: #333;">subs</span><span class="p">,</span> <span class="n" style="color: #333;">covers</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ncls</span><span class="p">.</span><span class="n" style="color: #333;">all_containments_both</span><span class="p">(</span><span class="n" style="color: #333;">starts</span><span class="p">,</span> <span class="n" style="color: #333;">ends</span><span class="p">,</span> <span class="n" style="color: #333;">ids</span><span class="p">)</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">ncls</span><span class="p">.</span><span class="n" style="color: #333;">intervals</span><span class="p">())</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"></span>
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<td class="diff-line-num new new_line" data-linenumber="81" 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">
81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">subs</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">covers</span><span class="p">)</span></span></pre>
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