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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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<strong><a href="https://salsa.debian.org/med-team/python-ncls/-/commit/eaea5e289b2f03b27162c052e58e0f442d4fa425">eaea5e28</a></strong>
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<span>by Nilesh Patra</span>
<i>at 2021-11-02T18:34:35+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.0.63+ds</pre>
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<h4>6 changed files:</h4>
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−
.travis.yml
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CHANGELOG
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ncls/__init__.py
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<a href="#9f5513a7b12c629ad6d3563e589e4ea34bfd934e">
ncls/src/ncls.pyx
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<a href="#bafd5c244f09a09f0ec4250726773d9b3b8c8db8">
ncls/src/ncls32.pyx
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<a href="#2472d5ab835e981576a859a20c8c459d3654e4c0">
ncls/version.py
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<h4>Changes:</h4>
<li id="dea01dd89a3b602828e630677fde5d77c06441c8">
<a href="https://salsa.debian.org/med-team/python-ncls/-/commit/eaea5e289b2f03b27162c052e58e0f442d4fa425#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</strong>
deleted
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">language</span><span class="pi">:</span> <span class="s" style="color: #d14;">python</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="yaml"><span class="na" style="color: #008080;">python</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="yaml"> <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">3.6"</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="yaml"><span class="na" style="color: #008080;">install</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pip install cython pytest</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">python setup.py install</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="yaml"></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># functionality is tested in the pyranges package</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="yaml"><span class="na" style="color: #008080;">script</span><span class="pi">:</span> <span class="s" style="color: #d14;">py.test tests/test_ncls.py && cd ~/ && python -c 'import ncls; print(ncls.__version__)'</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-ncls/-/commit/eaea5e289b2f03b27162c052e58e0f442d4fa425#1c497fbb3a46b78edf04cc2a2fa33f67e3ffbe2a"><strong>CHANGELOG</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"># 0.0.63 (18.10.21)</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">- fix critical error: fix 1024-error for subtract 64 bit</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"># 0.0.62 (20.09.21)</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">- fix critical error: fix 1024-error for subtract</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"># 0.0.61 (13.09.21)</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">- fix critical error: in case of more than 1024 overlaps for on interval only reported 1024 first</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"># 0.0.58/59/60 (hotfixes) (09.03.21)</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">- try to fix type mismatches and make causes more explicit</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"># 0.0.57 (14.10.20)</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">- accept lists/pd.Series in constructor</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/python-ncls/-/commit/eaea5e289b2f03b27162c052e58e0f442d4fa425#839e194c93fc74ef820f727ec630f6cd7783f9fa"><strong>ncls/__init__.py</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">@@ -8,10 +8,11 @@ def NCLS(starts, ends, ids):</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">starts</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">or</span> <span class="s" style="color: #d14;">"pandas"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="nb" style="color: #0086b3;">type</span><span class="p">(</span><span class="n" style="color: #333;">starts</span><span class="p">)):</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"> <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="o" style="font-weight: 600;">=</span> <span class="p">[</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="n" style="color: #333;">s</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">s</span> <span class="ow" style="font-weight: 600;">in</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="LC10" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC11" 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;">ids</span><span class="p">.</span><span class="n" style="color: #333;">astype</span><span class="p">(</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="LC12" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">starts</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="LC12" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">NCLS64</span><span class="p">(</span><span class="n" style="color: #333;">starts</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">ends</span></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="LC13" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">NCLS64</span><span class="p">(</span><span class="n" style="color: #333;">starts</span><span class="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">astype</span></span><span class="p"><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">int64</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="n" style="color: #333;"><span class="idiff">astype</span></span><span class="p"><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">int64</span></span><span class="p"><span class="idiff right">)</span>,</span> <span class="n" style="color: #333;">ids</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">starts</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;">int32</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">NCLS32</span><span class="p">(</span><span class="n" style="color: #333;">starts</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">ends</span></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="LC15" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">NCLS32</span><span class="p">(</span><span class="n" style="color: #333;">starts</span><span class="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">astype</span></span><span class="p"><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">int32</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="n" style="color: #333;"><span class="idiff">astype</span></span><span class="p"><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">int32</span></span><span class="p"><span class="idiff right">)</span>,</span> <span class="n" style="color: #333;">ids</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC16" 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="LC17" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">Exception</span><span class="p">(</span><span class="s" style="color: #d14;">"Starts/Ends not int64 or int32: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">starts</span><span class="p">.</span><span class="n" style="color: #333;">dtype</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"></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">@@ -24,7 +25,7 @@ def FNCLS(starts, ends, ids):</td>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"> <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="o" style="font-weight: 600;">=</span> <span class="p">[</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="n" style="color: #333;">s</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">s</span> <span class="ow" style="font-weight: 600;">in</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>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">starts</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;">double</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;">return</span> <span class="n" style="color: #333;">FNCLS</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="LC28" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">FNCLS</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 class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">astype</span></span><span class="p"><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">double</span></span><span class="p"><span class="idiff right">)</span>,</span> <span class="n" style="color: #333;">ids</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;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">Exception</span><span class="p">(</span><span class="s" style="color: #d14;">"Starts/Ends not double: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">starts</span><span class="p">.</span><span class="n" style="color: #333;">dtype</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"></span>
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<a href="https://salsa.debian.org/med-team/python-ncls/-/commit/eaea5e289b2f03b27162c052e58e0f442d4fa425#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">@@ -72,13 +72,17 @@ cdef class NCLS64:</td>
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<pre style="margin: 0;"> <span id="LC72" 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="LC73" 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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<pre style="margin: 0;"> <span id="LC74" 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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<pre style="margin: 0;">-<span id="LC75" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cpdef</span> <span class="nf" style="color: #900; font-weight: 600;">all_overlaps_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;">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;">indexes</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cpdef</span> <span class="nf" style="color: #900; font-weight: 600;">all_overlaps_both</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="cython"> <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>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="cython"> <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>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="cython"> <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;">indexes</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="cython"></span>
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<pre style="margin: 0;"> <span id="LC80" 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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<pre style="margin: 0;"> <span id="LC81" 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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<pre style="margin: 0;"> <span id="LC82" 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;">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">starts</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC83" 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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<pre style="margin: 0;"> <span id="LC84" 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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<pre style="margin: 0;">+<span id="LC85" 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;">spent</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="cython"></span>
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<pre style="margin: 0;"> <span id="LC87" 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;">int64</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC88" 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;">int64</span><span class="p">)</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">@@ -95,24 +99,17 @@ cdef class NCLS64:</td>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">im</span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;"># if empty</span></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="cython"> <span class="k" style="font-weight: 600;">return</span> <span class="p">[],</span> <span class="p">[]</span></span>
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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="cython"></span>
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># from time import time</span></span>
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># start = time()</span></span>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="cython"> <span class="n" style="color: #333;">it_alloc</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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<pre style="margin: 0;"> <span id="LC103" class="line" lang="cython"> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">it_alloc</span></span>
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102
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="cython"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">loop_counter</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="n" style="color: #333;">length</span><span class="p">):</span></span>
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103
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105
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="cython"></span>
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># print("loop_counter", loop_counter)</span></span>
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105
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># print("start", starts[loop_counter])</span></span>
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106
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># print("ends", ends[loop_counter])</span></span>
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107
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="cython"></span>
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108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># remember first pointer for dealloc</span></span>
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109
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="cython"> <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">it</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="106" 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">
106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="cython"> <span class="n" style="color: #333;">spent</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<td class="new_line diff-line-num new" data-linenumber="107" 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">
107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="cython"> <span class="k" style="font-weight: 600;">while</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">spent</span><span class="p">:</span></span>
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110
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<td class="new_line diff-line-num" data-linenumber="108" 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">
108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="cython"> <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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111
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<td class="new_line diff-line-num" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="cython"> <span class="n" style="color: #333;">cn</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">find_intervals</span><span class="p">(</span><span class="n" style="color: #333;">it</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">starts</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">],</span> <span class="kt" style="color: #458; font-weight: 600;">ends</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">],</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">im</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">ntop</span><span class="p">,</span></span>
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112
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<td class="new_line diff-line-num" data-linenumber="110" 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">
110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">subheader</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">nlists</span><span class="p">,</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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<td class="old_line diff-line-num" data-linenumber="113" 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">
113
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<td class="new_line diff-line-num" data-linenumber="111" 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">
111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="cython"> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">nhit</span><span class="p">),</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">it</span><span class="p">))</span> <span class="c1" style="color: #998; font-style: italic;"># GET NEXT BUFFER CHUNK</span></span>
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114
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112
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="cython"></span>
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115
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<td class="new_line diff-line-num old" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># print("nhit", nhit)</span></span>
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116
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<td class="new_line diff-line-num" data-linenumber="113" 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">
113
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">nfound</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">nhit</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">length</span><span class="p">:</span></span>
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117
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114
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="cython"></span>
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<td class="old_line diff-line-num" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
118
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<td class="new_line diff-line-num" data-linenumber="115" 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">
115
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="cython"> <span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">nhit</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="119" 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">@@ -122,11 +119,6 @@ cdef class NCLS64:</td>
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122
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119
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<pre style="margin: 0;"> <span id="LC119" 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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123
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120
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="cython"></span>
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124
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<td class="new_line diff-line-num" data-linenumber="121" 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">
121
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="cython"> <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nhit</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
125
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># print(" i", i)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
126
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<td class="new_line diff-line-num old" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="cython"></span>
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<td class="old_line diff-line-num old" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
127
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<td class="new_line diff-line-num old" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># print("length", length)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
128
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># print("nfound", nfound)</span></span>
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129
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># print("loop_counter", loop_counter)</span></span>
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130
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122
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="cython"> <span class="n" style="color: #333;">output</span><span class="p">[</span><span class="n" style="color: #333;">nfound</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">indexes</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">]</span></span>
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131
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<td class="new_line diff-line-num" data-linenumber="123" 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">
123
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="cython"> <span class="n" style="color: #333;">output_other</span><span class="p">[</span><span class="n" style="color: #333;">nfound</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">im_buf</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">target_id</span></span>
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<pre style="margin: 0;"> <span id="LC124" 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">@@ -136,13 +128,13 @@ cdef class NCLS64:</td>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="cython"> <span class="n" style="color: #333;">nfound</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="cython"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">nhit</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1024</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="cython"> <span class="n" style="color: #333;">spent</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="cython"></span>
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="cython"> <span class="n" style="color: #333;">cn</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">reset_interval_iterator</span><span class="p">(</span><span class="n" style="color: #333;">it_alloc</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="cython"> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">it_alloc</span></span>
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="cython"></span>
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="cython"> <span class="n" style="color: #333;">cn</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">free_interval_iterator</span><span class="p">(</span><span class="n" style="color: #333;">it_alloc</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># end = time()</span></span>
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="cython"></span>
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># print("ncls time:", end - start)</span></span>
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="cython"></span>
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="cython"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">output_arr</span><span class="p">[:</span><span class="n" style="color: #333;">nfound</span><span class="p">],</span> <span class="kt" style="color: #458; font-weight: 600;">output_arr_other</span><span class="p">[:</span><span class="n" style="color: #333;">nfound</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC140" 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">@@ -158,6 +150,7 @@ cdef class NCLS64:</td>
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158
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<pre style="margin: 0;"> <span id="LC150" 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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159
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151
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<pre style="margin: 0;"> <span id="LC151" 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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<pre style="margin: 0;"> <span id="LC152" 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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<pre style="margin: 0;">+<span id="LC153" 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;">spent</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="cython"></span>
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162
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155
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<pre style="margin: 0;"> <span id="LC155" 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;">int64</span><span class="p">)</span></span>
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163
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156
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<pre style="margin: 0;"> <span id="LC156" 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;">int64</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="170" 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">@@ -177,16 +170,14 @@ cdef class NCLS64:</td>
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177
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170
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="cython"> <span class="n" style="color: #333;">it_alloc</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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178
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171
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="cython"> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">it_alloc</span></span>
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179
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172
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="cython"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">loop_counter</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="n" style="color: #333;">length</span><span class="p">):</span></span>
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180
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="cython"></span>
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181
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># print("loop_counter", loop_counter)</span></span>
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182
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># remember first pointer for dealloc</span></span>
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183
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="cython"> <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">it</span><span class="p">:</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="cython"> <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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<td class="new_line diff-line-num new" data-linenumber="174" 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">
174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="cython"> <span class="n" style="color: #333;">spent</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<td class="new_line diff-line-num new" data-linenumber="175" 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">
175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="cython"> <span class="k" style="font-weight: 600;">while</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">spent</span><span class="p">:</span></span>
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184
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<td class="new_line diff-line-num" data-linenumber="176" 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">
176
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="cython"> <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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185
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<td class="new_line diff-line-num" data-linenumber="177" 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">
177
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="cython"> <span class="n" style="color: #333;">cn</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">find_intervals</span><span class="p">(</span><span class="n" style="color: #333;">it</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">starts</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">],</span> <span class="kt" style="color: #458; font-weight: 600;">ends</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">],</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">im</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">ntop</span><span class="p">,</span></span>
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186
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<td class="new_line diff-line-num" data-linenumber="178" 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">
178
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">subheader</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">nlists</span><span class="p">,</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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<td class="old_line diff-line-num" data-linenumber="187" 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">
187
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<td class="new_line diff-line-num" data-linenumber="179" 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">
179
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="cython"> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">nhit</span><span class="p">),</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">it</span><span class="p">))</span> <span class="c1" style="color: #998; font-style: italic;"># GET NEXT BUFFER CHUNK</span></span>
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188
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180
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">nhit</span><span class="p">:</span></span>
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189
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<td class="new_line diff-line-num old" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC189" class="line" lang="cython"> <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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190
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181
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="cython"> <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nhit</span><span class="p">:</span></span>
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<td class="old_line diff-line-num" data-linenumber="191" 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">
191
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<td class="new_line diff-line-num" data-linenumber="182" 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">
182
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">im_buf</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">max_end</span><span class="p">:</span></span>
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183
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># print("max_end", im_buf[i].end)</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="189" 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">@@ -198,6 +189,9 @@ cdef class NCLS64:</td>
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198
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189
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="cython"></span>
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199
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190
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="cython"> <span class="n" style="color: #333;">nfound</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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200
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191
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="cython"></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">nhit</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1024</span><span class="p">:</span></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="cython"> <span class="n" style="color: #333;">spent</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="cython"></span>
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201
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195
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="cython"> <span class="n" style="color: #333;">cn</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">reset_interval_iterator</span><span class="p">(</span><span class="n" style="color: #333;">it_alloc</span><span class="p">)</span></span>
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202
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196
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="cython"> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">it_alloc</span></span>
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203
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197
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="cython"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="210" 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">@@ -216,6 +210,7 @@ cdef class NCLS64:</td>
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216
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210
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<pre style="margin: 0;"> <span id="LC210" 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;">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">starts</span><span class="p">)</span></span>
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217
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211
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<pre style="margin: 0;"> <span id="LC211" 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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218
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212
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<pre style="margin: 0;"> <span id="LC212" 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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213
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<pre style="margin: 0;">+<span id="LC213" 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;">spent</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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219
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214
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="cython"></span>
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220
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<pre style="margin: 0;"> <span id="LC215" 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;">int64</span><span class="p">)</span></span>
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221
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216
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<pre style="margin: 0;"> <span id="LC216" 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;">int64</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="232" 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">@@ -237,16 +232,13 @@ cdef class NCLS64:</td>
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237
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="cython"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">loop_counter</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="n" style="color: #333;">length</span><span class="p">):</span></span>
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233
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<pre style="margin: 0;"> <span id="LC233" class="line" lang="cython"></span>
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239
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<pre style="margin: 0;"> <span id="LC234" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># remember first pointer for dealloc</span></span>
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240
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<pre style="margin: 0;">-<span id="LC240" class="line" lang="cython"> <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">it</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="cython"> <span class="n" style="color: #333;">spent</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<td class="new_line diff-line-num new" data-linenumber="236" 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">
236
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="cython"> <span class="k" style="font-weight: 600;">while</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">spent</span><span class="p">:</span></span>
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241
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237
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<pre style="margin: 0;"> <span id="LC237" class="line" lang="cython"> <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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242
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238
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<pre style="margin: 0;"> <span id="LC238" class="line" lang="cython"> <span class="n" style="color: #333;">cn</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">find_intervals</span><span class="p">(</span><span class="n" style="color: #333;">it</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">starts</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">],</span> <span class="kt" style="color: #458; font-weight: 600;">ends</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">],</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">im</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">ntop</span><span class="p">,</span></span>
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243
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<td class="new_line diff-line-num" data-linenumber="239" 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">
239
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<pre style="margin: 0;"> <span id="LC239" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">subheader</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">nlists</span><span class="p">,</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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244
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<td class="new_line diff-line-num" data-linenumber="240" 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">
240
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<pre style="margin: 0;"> <span id="LC240" class="line" lang="cython"> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">nhit</span><span class="p">),</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">it</span><span class="p">))</span> <span class="c1" style="color: #998; font-style: italic;"># GET NEXT BUFFER CHUNK</span></span>
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245
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241
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<pre style="margin: 0;"> <span id="LC241" class="line" lang="cython"></span>
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246
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<pre style="margin: 0;">-<span id="LC246" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># print("nhit", nhit)</span></span>
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247
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<pre style="margin: 0;">-<span id="LC247" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># print("length", length)</span></span>
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248
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<pre style="margin: 0;">-<span id="LC248" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># print("nfound", nfound)</span></span>
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249
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<pre style="margin: 0;">-<span id="LC249" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># print(nfound + nhit >= length)</span></span>
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250
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242
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<pre style="margin: 0;"> <span id="LC242" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">nfound</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">nhit</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">length</span><span class="p">:</span></span>
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251
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243
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<pre style="margin: 0;"> <span id="LC243" class="line" lang="cython"></span>
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252
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<td class="new_line diff-line-num" data-linenumber="244" 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">
244
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="cython"> <span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">nhit</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="258" 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">@@ -266,6 +258,9 @@ cdef class NCLS64:</td>
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266
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258
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<pre style="margin: 0;"> <span id="LC258" class="line" lang="cython"> <span class="n" style="color: #333;">nfound</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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267
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259
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<pre style="margin: 0;"> <span id="LC259" class="line" lang="cython"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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268
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260
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<pre style="margin: 0;"> <span id="LC260" class="line" lang="cython"></span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">nhit</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1024</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="cython"> <span class="n" style="color: #333;">spent</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span></span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="cython"></span>
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269
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264
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="cython"> <span class="n" style="color: #333;">cn</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">reset_interval_iterator</span><span class="p">(</span><span class="n" style="color: #333;">it_alloc</span><span class="p">)</span></span>
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270
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265
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="cython"> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">it_alloc</span></span>
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271
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266
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<pre style="margin: 0;"> <span id="LC266" class="line" lang="cython"></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="278" 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">@@ -283,6 +278,7 @@ cdef class NCLS64:</td>
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283
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278
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<pre style="margin: 0;"> <span id="LC278" 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;">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">starts</span><span class="p">)</span></span>
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284
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279
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<pre style="margin: 0;"> <span id="LC279" 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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285
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280
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<pre style="margin: 0;"> <span id="LC280" 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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<td class="new_line diff-line-num new" data-linenumber="281" 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">
281
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<pre style="margin: 0;">+<span id="LC281" 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;">spent</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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286
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282
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<pre style="margin: 0;"> <span id="LC282" class="line" lang="cython"></span>
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287
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283
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<pre style="margin: 0;"> <span id="LC283" 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;">int64</span><span class="p">)</span></span>
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288
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284
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<pre style="margin: 0;"> <span id="LC284" 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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="298" 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">@@ -302,7 +298,8 @@ cdef class NCLS64:</td>
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302
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298
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<pre style="margin: 0;"> <span id="LC298" class="line" lang="cython"></span>
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303
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299
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<pre style="margin: 0;"> <span id="LC299" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># remember first pointer for dealloc</span></span>
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304
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300
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<pre style="margin: 0;"> <span id="LC300" class="line" lang="cython"></span>
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305
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<pre style="margin: 0;">-<span id="LC305" class="line" lang="cython"> <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">it</span><span class="p">:</span></span>
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301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="cython"> <span class="n" style="color: #333;">spent</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="cython"> <span class="k" style="font-weight: 600;">while</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">spent</span><span class="p">:</span></span>
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306
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303
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<pre style="margin: 0;"> <span id="LC303" class="line" lang="cython"> <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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307
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304
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<pre style="margin: 0;"> <span id="LC304" class="line" lang="cython"> <span class="n" style="color: #333;">cn</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">find_intervals</span><span class="p">(</span><span class="n" style="color: #333;">it</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">starts</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">],</span> <span class="kt" style="color: #458; font-weight: 600;">ends</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">],</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">im</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">ntop</span><span class="p">,</span></span>
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308
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305
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<pre style="margin: 0;"> <span id="LC305" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">subheader</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">nlists</span><span class="p">,</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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="317" 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">@@ -320,6 +317,9 @@ cdef class NCLS64:</td>
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320
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<pre style="margin: 0;"> <span id="LC318" class="line" lang="cython"> <span class="n" style="color: #333;">nfound</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">nhit</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1024</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="cython"> <span class="n" style="color: #333;">spent</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;"> <span id="LC323" class="line" lang="cython"> <span class="n" style="color: #333;">cn</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">reset_interval_iterator</span><span class="p">(</span><span class="n" style="color: #333;">it_alloc</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC324" class="line" lang="cython"> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">it_alloc</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">@@ -344,13 +344,11 @@ cdef class NCLS64:</td>
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<pre style="margin: 0;"> <span id="LC344" 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;">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">starts</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC345" 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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<pre style="margin: 0;"> <span id="LC346" 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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<pre style="margin: 0;">+<span id="LC347" 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;">spent</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;">-<span id="LC348" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># output_arr = np.zeros(length, dtype=np.int64)</span></span>
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<pre style="margin: 0;"> <span id="LC349" class="line" lang="cython"> <span class="n" style="color: #333;">output_arr_length</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;">int64</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC350" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># cdef int64_t [::1] output</span></span>
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<pre style="margin: 0;"> <span id="LC350" 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_length</span></span>
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<pre style="margin: 0;"> <span id="LC351" class="line" lang="cython"></span>
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<pre style="margin: 0;">-<span id="LC353" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># output = output_arr</span></span>
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<pre style="margin: 0;"> <span id="LC352" class="line" lang="cython"> <span class="n" style="color: #333;">output_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">output_arr_length</span></span>
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<pre style="margin: 0;"> <span id="LC353" class="line" lang="cython"></span>
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<pre style="margin: 0;"> <span id="LC354" 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</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">@@ -367,7 +365,8 @@ cdef class NCLS64:</td>
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367
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<pre style="margin: 0;"> <span id="LC365" class="line" lang="cython"> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">starts</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">]</span></span>
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368
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<pre style="margin: 0;"> <span id="LC366" class="line" lang="cython"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ends</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC367" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># remember first pointer for dealloc</span></span>
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370
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<pre style="margin: 0;">-<span id="LC370" class="line" lang="cython"> <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">it</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="cython"> <span class="n" style="color: #333;">spent</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="cython"> <span class="k" style="font-weight: 600;">while</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">spent</span><span class="p">:</span></span>
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371
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370
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<pre style="margin: 0;"> <span id="LC370" class="line" lang="cython"> <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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372
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371
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<pre style="margin: 0;"> <span id="LC371" class="line" lang="cython"> <span class="n" style="color: #333;">cn</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">find_intervals</span><span class="p">(</span><span class="n" style="color: #333;">it</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">starts</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">],</span> <span class="kt" style="color: #458; font-weight: 600;">ends</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">],</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">im</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">ntop</span><span class="p">,</span></span>
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373
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372
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<pre style="margin: 0;"> <span id="LC372" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">subheader</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">nlists</span><span class="p">,</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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="376" 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">@@ -377,6 +376,8 @@ cdef class NCLS64:</td>
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377
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<pre style="margin: 0;"> <span id="LC376" class="line" lang="cython"> <span class="n" style="color: #333;">output_length</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nf" style="color: #900; font-weight: 600;">int_min</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">im_buf</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="nf" style="color: #900; font-weight: 600;">int_max</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">im_buf</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">start</span><span class="p">)</span></span>
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378
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<pre style="margin: 0;"> <span id="LC377" class="line" lang="cython"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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379
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<pre style="margin: 0;"> <span id="LC378" class="line" lang="cython"></span>
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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">nhit</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1024</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="cython"> <span class="n" style="color: #333;">spent</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span></span>
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381
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<pre style="margin: 0;"> <span id="LC381" class="line" lang="cython"></span>
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381
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382
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<pre style="margin: 0;"> <span id="LC382" class="line" lang="cython"> <span class="n" style="color: #333;">cn</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">reset_interval_iterator</span><span class="p">(</span><span class="n" style="color: #333;">it_alloc</span><span class="p">)</span></span>
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382
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383
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<pre style="margin: 0;"> <span id="LC383" class="line" lang="cython"> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">it_alloc</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="445" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="446" 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">@@ -445,7 +446,8 @@ cdef class NCLS64:</td>
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445
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446
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<pre style="margin: 0;"> <span id="LC446" 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="LC447" 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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<pre style="margin: 0;"> <span id="LC448" 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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<pre style="margin: 0;">-<span id="LC448" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cpdef</span> <span class="nf" style="color: #900; font-weight: 600;">set_difference_helper</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;">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;">indexes</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cpdef</span> <span class="nf" style="color: #900; font-weight: 600;">set_difference_helper</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;">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;">indexes</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;">nhits</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="cython"> <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;">nhits</span><span class="p">):</span></span>
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451
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<pre style="margin: 0;"> <span id="LC451" class="line" lang="cython"></span>
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<pre style="margin: 0;"> <span id="LC452" 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>
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<pre style="margin: 0;"> <span id="LC453" 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="458" 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">@@ -456,6 +458,7 @@ cdef class NCLS64:</td>
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<pre style="margin: 0;"> <span id="LC458" 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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459
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<pre style="margin: 0;"> <span id="LC459" 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;">overlap_type_nb</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;"> <span id="LC460" 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;">na</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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<pre style="margin: 0;">+<span id="LC461" 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;">spent</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;"> <span id="LC464" 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;">int64</span><span class="p">)</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">@@ -475,27 +478,21 @@ cdef class NCLS64:</td>
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<pre style="margin: 0;"> <span id="LC478" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">im</span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;"># if empty</span></span>
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<pre style="margin: 0;"> <span id="LC479" class="line" lang="cython"> <span class="k" style="font-weight: 600;">return</span> <span class="p">[],</span> <span class="p">[],</span> <span class="p">[]</span></span>
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<pre style="margin: 0;"> <span id="LC481" class="line" lang="cython"> <span class="n" style="color: #333;">it_alloc</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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482
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<pre style="margin: 0;"> <span id="LC482" class="line" lang="cython"> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">it_alloc</span></span>
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<pre style="margin: 0;"> <span id="LC483" class="line" lang="cython"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">loop_counter</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="n" style="color: #333;">length</span><span class="p">):</span></span>
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484
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<pre style="margin: 0;"> <span id="LC484" class="line" lang="cython"></span>
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<pre style="margin: 0;">-<span id="LC483" class="line" lang="cython"> <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">it</span><span class="p">:</span></span>
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485
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="cython"> <span class="n" style="color: #333;">nhit</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nhits</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">]</span></span>
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486
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="cython"> <span class="n" style="color: #333;">nstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">starts</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="cython"> <span class="n" style="color: #333;">nend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ends</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">]</span></span>
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488
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="cython"></span>
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489
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="cython"> <span class="k" style="font-weight: 600;">while</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 class="p">:</span></span>
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490
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<pre style="margin: 0;"> <span id="LC490" class="line" lang="cython"> <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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<pre style="margin: 0;"> <span id="LC491" class="line" lang="cython"> <span class="n" style="color: #333;">cn</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">find_intervals</span><span class="p">(</span><span class="n" style="color: #333;">it</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">starts</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">],</span> <span class="kt" style="color: #458; font-weight: 600;">ends</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">],</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">im</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">ntop</span><span class="p">,</span></span>
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486
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492
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<pre style="margin: 0;"> <span id="LC492" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">subheader</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">nlists</span><span class="p">,</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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<pre style="margin: 0;">-<span id="LC487" class="line" lang="cython"> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">nhit</span><span class="p">),</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">it</span><span class="p">))</span> <span class="c1" style="color: #998; font-style: italic;"># GET NEXT BUFFER CHUNK</span></span>
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<pre style="margin: 0;">-<span id="LC488" class="line" lang="cython"></span>
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<pre style="margin: 0;">-<span id="LC489" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;">#print("nhits:", nhit)</span></span>
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490
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<pre style="margin: 0;">-<span id="LC490" class="line" lang="cython"></span>
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491
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<pre style="margin: 0;">-<span id="LC491" class="line" lang="cython"> <span class="n" style="color: #333;">nstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">starts</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">]</span></span>
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492
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<pre style="margin: 0;">-<span id="LC492" class="line" lang="cython"> <span class="n" style="color: #333;">nend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ends</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">]</span></span>
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493
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<pre style="margin: 0;">-<span id="LC493" class="line" lang="cython"></span>
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494
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<pre style="margin: 0;">-<span id="LC494" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># print("nstart", nstart)</span></span>
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495
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<pre style="margin: 0;">-<span id="LC495" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># print("nend", nend)</span></span>
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493
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="cython"> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">na</span><span class="p">),</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">it</span><span class="p">))</span> <span class="c1" style="color: #998; font-style: italic;"># GET NEXT BUFFER CHUNK</span></span>
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496
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<pre style="margin: 0;"> <span id="LC494" class="line" lang="cython"></span>
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497
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<pre style="margin: 0;"> <span id="LC495" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">nfound</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">nhit</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">length</span><span class="p">:</span></span>
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498
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<pre style="margin: 0;">-<span id="LC498" class="line" lang="cython"></span>
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<pre style="margin: 0;"> <span id="LC496" class="line" lang="cython"> <span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">nhit</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span></span>
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500
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<pre style="margin: 0;"> <span id="LC497" 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;">resize</span><span class="p">(</span><span class="n" style="color: #333;">output_arr</span><span class="p">,</span> <span class="n" style="color: #333;">length</span><span class="p">)</span></span>
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501
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498
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<pre style="margin: 0;"> <span id="LC498" class="line" lang="cython"> <span class="n" style="color: #333;">output_arr_start</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;">resize</span><span class="p">(</span><span class="n" style="color: #333;">output_arr_start</span><span class="p">,</span> <span class="n" style="color: #333;">length</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="509" 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">@@ -512,62 +509,45 @@ cdef class NCLS64:</td>
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512
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509
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<pre style="margin: 0;"> <span id="LC509" class="line" lang="cython"> <span class="n" style="color: #333;">output</span><span class="p">[</span><span class="n" style="color: #333;">nfound</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">indexes</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">]</span></span>
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513
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510
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<pre style="margin: 0;"> <span id="LC510" class="line" lang="cython"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nhit</span></span>
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<pre style="margin: 0;"> <span id="LC511" class="line" lang="cython"> <span class="n" style="color: #333;">nfound</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="cython"> <span class="k" style="font-weight: 600;">break</span></span>
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513
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<pre style="margin: 0;"> <span id="LC513" class="line" lang="cython"></span>
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516
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<pre style="margin: 0;">-<span id="LC516" class="line" lang="cython"> <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nhit</span><span class="p">:</span></span>
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517
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<pre style="margin: 0;">-<span id="LC517" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># print("--- i:", i)</span></span>
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518
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<pre style="margin: 0;">-<span id="LC518" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># print("--- im_buf[i]", im_buf[i])</span></span>
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519
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<pre style="margin: 0;">-<span id="LC519" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;">#print(" B start:", im_buf[i].start)</span></span>
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520
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<pre style="margin: 0;">-<span id="LC520" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;">#print(" B end:", im_buf[i].end)</span></span>
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514
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<pre style="margin: 0;">+<span id="LC514" class="line" lang="cython"> <span class="n" style="color: #333;">max_i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1024</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">nhit</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1024</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">nhit</span></span>
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521
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515
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<pre style="margin: 0;"> <span id="LC515" class="line" lang="cython"></span>
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516
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="cython"> <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">max_i</span><span class="p">:</span></span>
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522
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517
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<pre style="margin: 0;"> <span id="LC517" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># in case the start contributes nothing</span></span>
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<pre style="margin: 0;">-<span id="LC523" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nhit</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>
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524
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<pre style="margin: 0;">-<span id="LC524" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># print(" i < nhit - 1")</span></span>
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518
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">nstart</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">im_buf</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">start</span><span class="p">:</span></span>
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519
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="cython"> <span class="n" style="color: #333;">output</span><span class="p">[</span><span class="n" style="color: #333;">nfound</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">indexes</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">]</span></span>
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520
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="cython"> <span class="n" style="color: #333;">output_start</span><span class="p">[</span><span class="n" style="color: #333;">nfound</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nstart</span></span>
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521
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="cython"> <span class="n" style="color: #333;">output_end</span><span class="p">[</span><span class="n" style="color: #333;">nfound</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">im_buf</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">start</span></span>
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522
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="cython"> <span class="n" style="color: #333;">nfound</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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523
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<pre style="margin: 0;">+<span id="LC523" class="line" lang="cython"> <span class="n" style="color: #333;">nstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">im_buf</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">end</span></span>
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524
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<pre style="margin: 0;">+<span id="LC524" class="line" lang="cython"></span>
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<pre style="margin: 0;">+<span id="LC525" class="line" lang="cython"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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526
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="cython"></span>
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<pre style="margin: 0;">+<span id="LC527" class="line" lang="cython"> <span class="n" style="color: #333;">nhit</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nhit</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1024</span></span>
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528
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<pre style="margin: 0;">+<span id="LC528" class="line" lang="cython"></span>
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529
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<pre style="margin: 0;">+<span id="LC529" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</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 class="p">:</span></span>
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530
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<pre style="margin: 0;">+<span id="LC530" class="line" lang="cython"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="new_line diff-line-num new" data-linenumber="531" 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">
531
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<pre style="margin: 0;">+<span id="LC531" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">im_buf</span><span class="p">[</span><span class="n" style="color: #333;">i</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;">nstart</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">im_buf</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">ends</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">]:</span></span>
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<pre style="margin: 0;">+<span id="LC532" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># print("im_buf[i].start <= nstart and im_buf[i].end >= ends[loop_counter]")</span></span>
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533
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<pre style="margin: 0;">+<span id="LC533" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;">#print("we are here " * 10)</span></span>
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525
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<pre style="margin: 0;"> <span id="LC534" class="line" lang="cython"></span>
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526
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<pre style="margin: 0;">-<span id="LC526" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">nstart</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">im_buf</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">start</span><span class="p">:</span></span>
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527
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<pre style="margin: 0;">-<span id="LC527" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;">#print(" new_start", nstart)</span></span>
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528
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<pre style="margin: 0;">-<span id="LC528" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;">#print(" new_end", im_buf[i].start)</span></span>
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535
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<pre style="margin: 0;">+<span id="LC535" class="line" lang="cython"> <span class="n" style="color: #333;">output_start</span><span class="p">[</span><span class="n" style="color: #333;">nfound</span><span class="p">]</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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<td class="new_line diff-line-num new" data-linenumber="536" 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">
536
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<pre style="margin: 0;">+<span id="LC536" class="line" lang="cython"> <span class="n" style="color: #333;">output_end</span><span class="p">[</span><span class="n" style="color: #333;">nfound</span><span class="p">]</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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<td class="new_line diff-line-num new" data-linenumber="537" 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">
537
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="cython"> <span class="n" style="color: #333;">output</span><span class="p">[</span><span class="n" style="color: #333;">nfound</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;"><</span><span class="nb" style="color: #0086b3;">long</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">indexes</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="538" 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">
538
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<pre style="margin: 0;">+<span id="LC538" class="line" lang="cython"> <span class="n" style="color: #333;">nfound</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="new_line diff-line-num new" data-linenumber="539" 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">
539
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<pre style="margin: 0;">+<span id="LC539" class="line" lang="cython"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="540" 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">
540
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<pre style="margin: 0;">+<span id="LC540" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">im_buf</span><span class="p">[</span><span class="n" style="color: #333;">i</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;">nstart</span><span class="p">:</span></span>
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529
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<td class="new_line diff-line-num" data-linenumber="541" 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">
541
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<pre style="margin: 0;"> <span id="LC541" class="line" lang="cython"> <span class="n" style="color: #333;">output</span><span class="p">[</span><span class="n" style="color: #333;">nfound</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">indexes</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">]</span></span>
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530
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542
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<pre style="margin: 0;"> <span id="LC542" class="line" lang="cython"> <span class="n" style="color: #333;">output_start</span><span class="p">[</span><span class="n" style="color: #333;">nfound</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nstart</span></span>
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531
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543
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<pre style="margin: 0;"> <span id="LC543" class="line" lang="cython"> <span class="n" style="color: #333;">output_end</span><span class="p">[</span><span class="n" style="color: #333;">nfound</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">im_buf</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">start</span></span>
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532
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544
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<pre style="margin: 0;"> <span id="LC544" class="line" lang="cython"> <span class="n" style="color: #333;">nfound</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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533
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545
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<pre style="margin: 0;"> <span id="LC545" class="line" lang="cython"></span>
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534
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<pre style="margin: 0;">-<span id="LC534" class="line" lang="cython"> <span class="n" style="color: #333;">nstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">im_buf</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">end</span></span>
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535
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<pre style="margin: 0;">-<span id="LC535" class="line" lang="cython"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">nhit</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>
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536
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<pre style="margin: 0;">-<span id="LC536" class="line" lang="cython"></span>
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537
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<td class="new_line diff-line-num old" data-linenumber="546" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC537" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># print("i == nhit -1")</span></span>
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538
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<td class="new_line diff-line-num old" data-linenumber="546" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC538" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;">#print("im_buf[i].start", im_buf[i].start)</span></span>
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539
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<td class="new_line diff-line-num old" data-linenumber="546" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC539" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;">#print("im_buf[i].end", im_buf[i].end)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="540" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
540
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<td class="new_line diff-line-num old" data-linenumber="546" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC540" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;">#print("nstart", nstart)</span></span>
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541
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<td class="new_line diff-line-num old" data-linenumber="546" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC541" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;">#print("ends[loop_counter]", ends[loop_counter])</span></span>
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542
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<pre style="margin: 0;">-<span id="LC542" class="line" lang="cython"></span>
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543
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<pre style="margin: 0;">-<span id="LC543" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">im_buf</span><span class="p">[</span><span class="n" style="color: #333;">i</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;">nstart</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">im_buf</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">ends</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">]:</span></span>
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<pre style="margin: 0;">-<span id="LC544" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># print("im_buf[i].start <= nstart and im_buf[i].end >= ends[loop_counter]")</span></span>
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545
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<pre style="margin: 0;">-<span id="LC545" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;">#print("we are here " * 10)</span></span>
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546
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<pre style="margin: 0;">-<span id="LC546" class="line" lang="cython"></span>
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547
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<td class="new_line diff-line-num old" data-linenumber="546" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC547" class="line" lang="cython"> <span class="n" style="color: #333;">output_start</span><span class="p">[</span><span class="n" style="color: #333;">nfound</span><span class="p">]</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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548
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<td class="new_line diff-line-num old" data-linenumber="546" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC548" class="line" lang="cython"> <span class="n" style="color: #333;">output_end</span><span class="p">[</span><span class="n" style="color: #333;">nfound</span><span class="p">]</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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549
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<td class="new_line diff-line-num old" data-linenumber="546" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC549" class="line" lang="cython"> <span class="n" style="color: #333;">output</span><span class="p">[</span><span class="n" style="color: #333;">nfound</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;"><</span><span class="nb" style="color: #0086b3;">long</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">indexes</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="546" 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">
546
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">im_buf</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">ends</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">]:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="547" 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">
547
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<pre style="margin: 0;">+<span id="LC547" class="line" lang="cython"> <span class="n" style="color: #333;">output</span><span class="p">[</span><span class="n" style="color: #333;">nfound</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">indexes</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">]</span></span>
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548
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<pre style="margin: 0;">+<span id="LC548" class="line" lang="cython"> <span class="n" style="color: #333;">output_start</span><span class="p">[</span><span class="n" style="color: #333;">nfound</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">im_buf</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">end</span></span>
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549
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="cython"> <span class="n" style="color: #333;">output_end</span><span class="p">[</span><span class="n" style="color: #333;">nfound</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ends</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">]</span></span>
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550
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<pre style="margin: 0;"> <span id="LC550" class="line" lang="cython"> <span class="n" style="color: #333;">nfound</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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551
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<td class="new_line diff-line-num old" data-linenumber="551" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC551" class="line" lang="cython"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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552
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<td class="new_line diff-line-num old" data-linenumber="551" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC552" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">im_buf</span><span class="p">[</span><span class="n" style="color: #333;">i</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;">nstart</span><span class="p">:</span></span>
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553
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<td class="new_line diff-line-num old" data-linenumber="551" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC553" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># print("im_buf[i].start > nstart", im_buf[i].start, nstart)</span></span>
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554
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<pre style="margin: 0;">-<span id="LC554" class="line" lang="cython"> <span class="n" style="color: #333;">output</span><span class="p">[</span><span class="n" style="color: #333;">nfound</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">indexes</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">]</span></span>
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555
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<pre style="margin: 0;">-<span id="LC555" class="line" lang="cython"> <span class="n" style="color: #333;">output_start</span><span class="p">[</span><span class="n" style="color: #333;">nfound</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nstart</span></span>
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556
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<pre style="margin: 0;">-<span id="LC556" class="line" lang="cython"> <span class="n" style="color: #333;">output_end</span><span class="p">[</span><span class="n" style="color: #333;">nfound</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">im_buf</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">start</span></span>
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557
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<td class="new_line diff-line-num old" data-linenumber="551" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC557" class="line" lang="cython"> <span class="n" style="color: #333;">nfound</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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558
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<pre style="margin: 0;">-<span id="LC558" class="line" lang="cython"></span>
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559
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<pre style="margin: 0;">-<span id="LC559" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">im_buf</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">ends</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">]:</span></span>
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<pre style="margin: 0;">-<span id="LC560" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># print("im_buf[i].end < ends[loop_counter]", im_buf[i].end, ends[loop_counter])</span></span>
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561
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<pre style="margin: 0;">-<span id="LC561" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># print("i, loop_counter", i, loop_counter)</span></span>
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562
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<pre style="margin: 0;">-<span id="LC562" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># print("indexes[loop_counter]", indexes[loop_counter])</span></span>
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<pre style="margin: 0;">-<span id="LC563" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># print("indexes", indexes[loop_counte rloop_counter])</span></span>
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564
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<pre style="margin: 0;">-<span id="LC564" class="line" lang="cython"></span>
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565
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<pre style="margin: 0;">-<span id="LC565" class="line" lang="cython"> <span class="n" style="color: #333;">output</span><span class="p">[</span><span class="n" style="color: #333;">nfound</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">indexes</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">]</span></span>
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566
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<pre style="margin: 0;">-<span id="LC566" class="line" lang="cython"> <span class="n" style="color: #333;">output_start</span><span class="p">[</span><span class="n" style="color: #333;">nfound</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">im_buf</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">end</span></span>
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567
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<pre style="margin: 0;">-<span id="LC567" class="line" lang="cython"> <span class="n" style="color: #333;">output_end</span><span class="p">[</span><span class="n" style="color: #333;">nfound</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ends</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">]</span></span>
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568
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<pre style="margin: 0;">-<span id="LC568" class="line" lang="cython"> <span class="n" style="color: #333;">nfound</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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569
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<pre style="margin: 0;">-<span id="LC569" class="line" lang="cython"></span>
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<pre style="margin: 0;">-<span id="LC570" class="line" lang="cython"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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571
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551
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<pre style="margin: 0;"> <span id="LC551" class="line" lang="cython"></span>
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552
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<pre style="margin: 0;"> <span id="LC552" class="line" lang="cython"> <span class="n" style="color: #333;">cn</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">reset_interval_iterator</span><span class="p">(</span><span class="n" style="color: #333;">it_alloc</span><span class="p">)</span></span>
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553
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<pre style="margin: 0;"> <span id="LC553" class="line" lang="cython"> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">it_alloc</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="609" 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">@@ -629,6 +609,7 @@ cdef class NCLS64:</td>
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629
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609
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<pre style="margin: 0;"> <span id="LC609" 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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630
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610
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<pre style="margin: 0;"> <span id="LC610" 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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611
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<pre style="margin: 0;"> <span id="LC611" 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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612
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<pre style="margin: 0;">+<span id="LC612" 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;">spent</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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632
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613
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<pre style="margin: 0;"> <span id="LC613" class="line" lang="cython"></span>
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614
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<pre style="margin: 0;"> <span id="LC614" 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;">int64</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC615" 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;">int64</span><span class="p">)</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">@@ -654,7 +635,8 @@ cdef class NCLS64:</td>
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<pre style="margin: 0;"> <span id="LC635" class="line" lang="cython"></span>
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<pre style="margin: 0;"> <span id="LC636" class="line" lang="cython"> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">starts</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC637" class="line" lang="cython"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ends</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC657" class="line" lang="cython"> <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">it</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC638" class="line" lang="cython"> <span class="n" style="color: #333;">spent</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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639
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<pre style="margin: 0;">+<span id="LC639" class="line" lang="cython"> <span class="k" style="font-weight: 600;">while</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">spent</span><span class="p">:</span></span>
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658
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<pre style="margin: 0;"> <span id="LC640" class="line" lang="cython"> <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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<pre style="margin: 0;"> <span id="LC641" class="line" lang="cython"> <span class="n" style="color: #333;">cn</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">find_intervals</span><span class="p">(</span><span class="n" style="color: #333;">it</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="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">im</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">ntop</span><span class="p">,</span></span>
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660
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<pre style="margin: 0;"> <span id="LC642" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">subheader</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">nlists</span><span class="p">,</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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="678" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="660" 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">@@ -678,6 +660,9 @@ cdef class NCLS64:</td>
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<pre style="margin: 0;"> <span id="LC660" class="line" lang="cython"> <span class="n" style="color: #333;">nfound</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;"> <span id="LC661" class="line" lang="cython"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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662
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<pre style="margin: 0;"> <span id="LC662" class="line" lang="cython"></span>
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<pre style="margin: 0;">+<span id="LC663" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">nhit</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1024</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC664" class="line" lang="cython"> <span class="n" style="color: #333;">spent</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">+<span id="LC665" class="line" lang="cython"></span>
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<pre style="margin: 0;"> <span id="LC666" class="line" lang="cython"> <span class="n" style="color: #333;">cn</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">reset_interval_iterator</span><span class="p">(</span><span class="n" style="color: #333;">it_alloc</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC667" class="line" lang="cython"> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">it_alloc</span></span>
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<pre style="margin: 0;"> <span id="LC668" class="line" lang="cython"></span>
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<a href="https://salsa.debian.org/med-team/python-ncls/-/commit/eaea5e289b2f03b27162c052e58e0f442d4fa425#bafd5c244f09a09f0ec4250726773d9b3b8c8db8"><strong>ncls/src/ncls32.pyx</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -73,13 +73,17 @@ cdef class NCLS32:</td>
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<pre style="margin: 0;"> <span id="LC73" 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="LC74" 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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<pre style="margin: 0;"> <span id="LC75" 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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<pre style="margin: 0;">-<span id="LC76" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cpdef</span> <span class="nf" style="color: #900; font-weight: 600;">all_overlaps_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;">int32_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;">int32_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;">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;">indexes</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cpdef</span> <span class="nf" style="color: #900; font-weight: 600;">all_overlaps_both</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="cython"> <span class="kt" style="color: #458; font-weight: 600;">const</span> <span class="n" style="color: #333;">int32_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>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="cython"> <span class="kt" style="color: #458; font-weight: 600;">const</span> <span class="n" style="color: #333;">int32_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>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="cython"> <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;">indexes</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="cython"></span>
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<pre style="margin: 0;"> <span id="LC81" 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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79
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<pre style="margin: 0;"> <span id="LC82" 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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<pre style="margin: 0;"> <span id="LC83" 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;">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">starts</span><span class="p">)</span></span>
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81
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<pre style="margin: 0;"> <span id="LC84" 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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82
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<pre style="margin: 0;"> <span id="LC85" 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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<pre style="margin: 0;">+<span id="LC86" 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;">spent</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="cython"></span>
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<pre style="margin: 0;"> <span id="LC88" 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;">long</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC89" 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;">long</span><span class="p">)</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">@@ -100,8 +104,9 @@ cdef class NCLS32:</td>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="cython"> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">it_alloc</span></span>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="cython"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">loop_counter</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="n" style="color: #333;">length</span><span class="p">):</span></span>
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102
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106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="cython"></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="cython"> <span class="n" style="color: #333;">spent</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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103
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108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># remember first pointer for dealloc</span></span>
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104
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="cython"> <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;"><span class="idiff left right">i</span>t</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="109" 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">
109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="cython"> <span class="k" style="font-weight: 600;">while</span> <span class="ow" style="font-weight: 600;"><span class="idiff left">not</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">spen</span>t</span><span class="p">:</span></span>
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105
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<td class="new_line diff-line-num" data-linenumber="110" 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">
110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="cython"> <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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106
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<td class="new_line diff-line-num" data-linenumber="111" 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">
111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="cython"> <span class="n" style="color: #333;">cn</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">find_intervals</span><span class="p">(</span><span class="n" style="color: #333;">it</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">starts</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">],</span> <span class="kt" style="color: #458; font-weight: 600;">ends</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">],</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">im</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">ntop</span><span class="p">,</span></span>
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107
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112
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">subheader</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">nlists</span><span class="p">,</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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="135" 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">@@ -130,6 +135,10 @@ cdef class NCLS32:</td>
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130
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135
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="cython"> <span class="n" style="color: #333;">nfound</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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131
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136
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="cython"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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132
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137
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="cython"></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">nhit</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1024</span><span class="p">:</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="cython"> <span class="n" style="color: #333;">spent</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="cython"></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="cython"></span>
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133
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142
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="cython"> <span class="n" style="color: #333;">cn</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">reset_interval_iterator</span><span class="p">(</span><span class="n" style="color: #333;">it_alloc</span><span class="p">)</span></span>
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134
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143
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="cython"> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">it_alloc</span></span>
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135
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144
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="cython"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="157" 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">@@ -148,6 +157,7 @@ cdef class NCLS32:</td>
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148
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157
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<pre style="margin: 0;"> <span id="LC157" 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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149
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158
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<pre style="margin: 0;"> <span id="LC158" 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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150
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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;">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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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;">spent</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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151
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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;">long</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;">long</span><span class="p">)</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">@@ -170,13 +180,14 @@ cdef class NCLS32:</td>
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170
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180
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="cython"></span>
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171
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># print("loop_counter", loop_counter)</span></span>
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172
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182
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># remember first pointer for dealloc</span></span>
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173
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="cython"> <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">it</span><span class="p">:</span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="cython"> <span class="n" style="color: #333;">spent</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="cython"> <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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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="cython"> <span class="k" style="font-weight: 600;">while</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">spent</span><span class="p">:</span></span>
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174
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186
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="cython"> <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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175
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187
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<pre style="margin: 0;"> <span id="LC187" class="line" lang="cython"> <span class="n" style="color: #333;">cn</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">find_intervals</span><span class="p">(</span><span class="n" style="color: #333;">it</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">starts</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">],</span> <span class="kt" style="color: #458; font-weight: 600;">ends</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">],</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">im</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">ntop</span><span class="p">,</span></span>
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176
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188
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">subheader</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">nlists</span><span class="p">,</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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177
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189
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="cython"> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">nhit</span><span class="p">),</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">it</span><span class="p">))</span> <span class="c1" style="color: #998; font-style: italic;"># GET NEXT BUFFER CHUNK</span></span>
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178
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190
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="cython"></span>
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179
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="cython"> <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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180
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191
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="cython"></span>
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181
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># """Finding last overlap in NCLS: iterate from start, find last maximal end."""</span></span>
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182
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<pre style="margin: 0;"> <span id="LC193" 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">@@ -192,6 +203,9 @@ cdef class NCLS32:</td>
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203
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="cython"></span>
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="cython"> <span class="n" style="color: #333;">nfound</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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205
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="cython"></span>
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">nhit</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1024</span><span class="p">:</span></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="cython"> <span class="n" style="color: #333;">spent</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="cython"></span>
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195
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209
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="cython"> <span class="n" style="color: #333;">cn</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">reset_interval_iterator</span><span class="p">(</span><span class="n" style="color: #333;">it_alloc</span><span class="p">)</span></span>
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196
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210
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="cython"> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">it_alloc</span></span>
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197
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211
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="cython"></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="224" 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">@@ -210,6 +224,7 @@ cdef class NCLS32:</td>
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210
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224
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<pre style="margin: 0;"> <span id="LC224" 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;">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">starts</span><span class="p">)</span></span>
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211
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<pre style="margin: 0;"> <span id="LC225" 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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212
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<pre style="margin: 0;"> <span id="LC226" 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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227
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<pre style="margin: 0;">+<span id="LC227" 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;">spent</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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213
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228
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<pre style="margin: 0;"> <span id="LC228" class="line" lang="cython"></span>
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214
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<pre style="margin: 0;"> <span id="LC229" 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;">long</span><span class="p">)</span></span>
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215
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<pre style="margin: 0;"> <span id="LC230" 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;">long</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="246" 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">@@ -231,7 +246,8 @@ cdef class NCLS32:</td>
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231
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="cython"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">loop_counter</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="n" style="color: #333;">length</span><span class="p">):</span></span>
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232
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247
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<pre style="margin: 0;"> <span id="LC247" class="line" lang="cython"></span>
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># remember first pointer for dealloc</span></span>
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<pre style="margin: 0;">-<span id="LC234" class="line" lang="cython"> <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">it</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="249" 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">
249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="cython"> <span class="n" style="color: #333;">spent</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="cython"> <span class="k" style="font-weight: 600;">while</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">spent</span><span class="p">:</span></span>
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235
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<td class="new_line diff-line-num" data-linenumber="251" 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">
251
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<pre style="margin: 0;"> <span id="LC251" class="line" lang="cython"> <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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236
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<td class="new_line diff-line-num" data-linenumber="252" 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">
252
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<pre style="margin: 0;"> <span id="LC252" class="line" lang="cython"> <span class="n" style="color: #333;">cn</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">find_intervals</span><span class="p">(</span><span class="n" style="color: #333;">it</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">starts</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">],</span> <span class="kt" style="color: #458; font-weight: 600;">ends</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">],</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">im</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">ntop</span><span class="p">,</span></span>
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237
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<td class="new_line diff-line-num" data-linenumber="253" 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">
253
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<pre style="margin: 0;"> <span id="LC253" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">subheader</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">nlists</span><span class="p">,</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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="279" 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">@@ -263,6 +279,9 @@ cdef class NCLS32:</td>
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263
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279
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<pre style="margin: 0;"> <span id="LC279" class="line" lang="cython"> <span class="n" style="color: #333;">nfound</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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264
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280
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<pre style="margin: 0;"> <span id="LC280" class="line" lang="cython"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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265
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281
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<pre style="margin: 0;"> <span id="LC281" class="line" lang="cython"></span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">nhit</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1024</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="283" 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">
283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="cython"> <span class="n" style="color: #333;">spent</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span></span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="cython"></span>
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266
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285
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<pre style="margin: 0;"> <span id="LC285" class="line" lang="cython"> <span class="n" style="color: #333;">cn</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">reset_interval_iterator</span><span class="p">(</span><span class="n" style="color: #333;">it_alloc</span><span class="p">)</span></span>
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267
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286
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<pre style="margin: 0;"> <span id="LC286" class="line" lang="cython"> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">it_alloc</span></span>
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268
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287
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<pre style="margin: 0;"> <span id="LC287" class="line" lang="cython"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="301" 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">@@ -282,6 +301,7 @@ cdef class NCLS32:</td>
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282
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301
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<pre style="margin: 0;"> <span id="LC301" 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;">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">starts</span><span class="p">)</span></span>
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283
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302
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<pre style="margin: 0;"> <span id="LC302" 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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284
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303
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<pre style="margin: 0;"> <span id="LC303" 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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<td class="new_line diff-line-num new" data-linenumber="304" 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">
304
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<pre style="margin: 0;">+<span id="LC304" 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;">spent</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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285
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305
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<pre style="margin: 0;"> <span id="LC305" class="line" lang="cython"></span>
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286
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306
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<pre style="margin: 0;"> <span id="LC306" 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;">long</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC307" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">long</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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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="321" 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">@@ -301,7 +321,8 @@ cdef class NCLS32:</td>
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321
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<pre style="margin: 0;"> <span id="LC321" class="line" lang="cython"></span>
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302
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<pre style="margin: 0;"> <span id="LC322" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># remember first pointer for dealloc</span></span>
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323
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<pre style="margin: 0;"> <span id="LC323" class="line" lang="cython"></span>
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<pre style="margin: 0;">-<span id="LC304" class="line" lang="cython"> <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">it</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="cython"> <span class="n" style="color: #333;">spent</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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325
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="cython"> <span class="k" style="font-weight: 600;">while</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">spent</span><span class="p">:</span></span>
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305
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<pre style="margin: 0;"> <span id="LC326" class="line" lang="cython"> <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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306
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327
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<pre style="margin: 0;"> <span id="LC327" class="line" lang="cython"> <span class="n" style="color: #333;">cn</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">find_intervals</span><span class="p">(</span><span class="n" style="color: #333;">it</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">starts</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">],</span> <span class="kt" style="color: #458; font-weight: 600;">ends</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">],</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">im</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">ntop</span><span class="p">,</span></span>
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307
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328
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<pre style="margin: 0;"> <span id="LC328" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">subheader</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">nlists</span><span class="p">,</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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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="340" 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">@@ -319,6 +340,9 @@ cdef class NCLS32:</td>
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319
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<pre style="margin: 0;"> <span id="LC340" class="line" lang="cython"></span>
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<pre style="margin: 0;"> <span id="LC341" class="line" lang="cython"> <span class="n" style="color: #333;">nfound</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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342
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<pre style="margin: 0;"> <span id="LC342" class="line" lang="cython"></span>
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">nhit</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1024</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="cython"> <span class="n" style="color: #333;">spent</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="cython"></span>
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<pre style="margin: 0;"> <span id="LC346" class="line" lang="cython"> <span class="n" style="color: #333;">cn</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">reset_interval_iterator</span><span class="p">(</span><span class="n" style="color: #333;">it_alloc</span><span class="p">)</span></span>
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323
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<pre style="margin: 0;"> <span id="LC347" class="line" lang="cython"> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">it_alloc</span></span>
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348
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<pre style="margin: 0;"> <span id="LC348" class="line" lang="cython"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="343" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="367" 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">@@ -343,6 +367,7 @@ cdef class NCLS32:</td>
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343
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<pre style="margin: 0;"> <span id="LC367" 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;">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">starts</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC368" 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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345
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369
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<pre style="margin: 0;"> <span id="LC369" 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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370
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<pre style="margin: 0;">+<span id="LC370" 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;">spent</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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346
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371
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<pre style="margin: 0;"> <span id="LC371" class="line" lang="cython"></span>
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347
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372
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<pre style="margin: 0;"> <span id="LC372" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># output_arr = np.zeros(length, dtype=long)</span></span>
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348
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373
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<pre style="margin: 0;"> <span id="LC373" class="line" lang="cython"> <span class="n" style="color: #333;">output_arr_length</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;">long</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="391" 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">@@ -366,7 +391,8 @@ cdef class NCLS32:</td>
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366
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391
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<pre style="margin: 0;"> <span id="LC391" class="line" lang="cython"> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">starts</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">]</span></span>
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367
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392
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<pre style="margin: 0;"> <span id="LC392" class="line" lang="cython"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ends</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">]</span></span>
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368
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393
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<pre style="margin: 0;"> <span id="LC393" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># remember first pointer for dealloc</span></span>
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369
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<pre style="margin: 0;">-<span id="LC369" class="line" lang="cython"> <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">it</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="cython"> <span class="n" style="color: #333;">spent</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<td class="new_line diff-line-num new" data-linenumber="395" 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">
395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="cython"> <span class="k" style="font-weight: 600;">while</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">spent</span><span class="p">:</span></span>
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370
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396
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<pre style="margin: 0;"> <span id="LC396" class="line" lang="cython"> <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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371
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397
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<pre style="margin: 0;"> <span id="LC397" class="line" lang="cython"> <span class="n" style="color: #333;">cn</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">find_intervals</span><span class="p">(</span><span class="n" style="color: #333;">it</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">starts</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">],</span> <span class="kt" style="color: #458; font-weight: 600;">ends</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">],</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">im</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">ntop</span><span class="p">,</span></span>
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372
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398
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<pre style="margin: 0;"> <span id="LC398" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">subheader</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">nlists</span><span class="p">,</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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="376" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="402" 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">@@ -376,6 +402,8 @@ cdef class NCLS32:</td>
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376
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402
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<pre style="margin: 0;"> <span id="LC402" class="line" lang="cython"> <span class="n" style="color: #333;">output_length</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nf" style="color: #900; font-weight: 600;">int_min</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">im_buf</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="nf" style="color: #900; font-weight: 600;">int_max</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">im_buf</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">start</span><span class="p">)</span></span>
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377
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403
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<pre style="margin: 0;"> <span id="LC403" class="line" lang="cython"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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378
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404
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<pre style="margin: 0;"> <span id="LC404" class="line" lang="cython"></span>
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405
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">nhit</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1024</span><span class="p">:</span></span>
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406
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="cython"> <span class="n" style="color: #333;">spent</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span></span>
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379
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407
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<pre style="margin: 0;"> <span id="LC407" class="line" lang="cython"></span>
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380
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408
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<pre style="margin: 0;"> <span id="LC408" class="line" lang="cython"> <span class="n" style="color: #333;">cn</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">reset_interval_iterator</span><span class="p">(</span><span class="n" style="color: #333;">it_alloc</span><span class="p">)</span></span>
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381
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409
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<pre style="margin: 0;"> <span id="LC409" class="line" lang="cython"> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">it_alloc</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="472" 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">@@ -444,7 +472,8 @@ cdef class NCLS32:</td>
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444
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472
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<pre style="margin: 0;"> <span id="LC472" 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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445
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473
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<pre style="margin: 0;"> <span id="LC473" 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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446
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474
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<pre style="margin: 0;"> <span id="LC474" 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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447
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<pre style="margin: 0;">-<span id="LC447" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cpdef</span> <span class="nf" style="color: #900; font-weight: 600;">set_difference_helper</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;">int32_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;">int32_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;">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;">indexes</span><span class="p">):</span></span>
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475
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cpdef</span> <span class="nf" style="color: #900; font-weight: 600;">set_difference_helper</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;">int32_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;">int32_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;">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;">indexes</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="cython"> <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;">nhits</span><span class="p">):</span></span>
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448
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477
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<pre style="margin: 0;"> <span id="LC477" class="line" lang="cython"></span>
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478
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<pre style="margin: 0;"> <span id="LC478" 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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450
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479
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<pre style="margin: 0;"> <span id="LC479" 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 old_line" data-linenumber="452" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="481" 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">@@ -452,10 +481,10 @@ cdef class NCLS32:</td>
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452
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481
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<pre style="margin: 0;"> <span id="LC481" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">nstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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453
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482
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<pre style="margin: 0;"> <span id="LC482" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">nend</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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454
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483
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<pre style="margin: 0;"> <span id="LC483" 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;">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">starts</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC455" 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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456
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484
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<pre style="margin: 0;"> <span id="LC484" 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;">overlap_type_nb</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;"> <span id="LC485" 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;">na</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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458
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<pre style="margin: 0;">-<span id="LC458" class="line" lang="cython"></span>
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486
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<pre style="margin: 0;">+<span id="LC486" 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;">spent</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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487
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<pre style="margin: 0;">+<span id="LC487" 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_i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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459
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488
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<pre style="margin: 0;"> <span id="LC488" class="line" lang="cython"></span>
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<pre style="margin: 0;"> <span id="LC489" 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;">int64</span><span class="p">)</span></span>
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461
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490
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<pre style="margin: 0;"> <span id="LC490" class="line" lang="cython"> <span class="n" style="color: #333;">output_arr_start</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;">int32</span><span class="p">)</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">@@ -476,30 +505,21 @@ cdef class NCLS32:</td>
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476
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505
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<pre style="margin: 0;"> <span id="LC505" class="line" lang="cython"></span>
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477
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<pre style="margin: 0;"> <span id="LC506" class="line" lang="cython"> <span class="n" style="color: #333;">it_alloc</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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478
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507
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<pre style="margin: 0;"> <span id="LC507" class="line" lang="cython"> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">it_alloc</span></span>
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<pre style="margin: 0;">-<span id="LC479" class="line" lang="cython"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">loop_counter</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="n" style="color: #333;">length</span><span class="p">):</span></span>
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480
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<pre style="margin: 0;">-<span id="LC480" class="line" lang="cython"></span>
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481
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<pre style="margin: 0;">-<span id="LC481" class="line" lang="cython"> <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">it</span><span class="p">:</span></span>
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482
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<pre style="margin: 0;">-<span id="LC482" class="line" lang="cython"> <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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483
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508
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<pre style="margin: 0;"> <span id="LC508" class="line" lang="cython"></span>
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484
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<pre style="margin: 0;">-<span id="LC484" class="line" lang="cython"> <span class="n" style="color: #333;">nstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">starts</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">]</span></span>
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485
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<pre style="margin: 0;">-<span id="LC485" class="line" lang="cython"> <span class="n" style="color: #333;">nend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ends</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">]</span></span>
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509
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<pre style="margin: 0;">+<span id="LC509" class="line" lang="cython"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">loop_counter</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="n" style="color: #333;">length</span><span class="p">):</span></span>
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486
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510
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<pre style="margin: 0;"> <span id="LC510" class="line" lang="cython"></span>
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487
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<pre style="margin: 0;">-<span id="LC487" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># print("----" * 5)</span></span>
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488
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<pre style="margin: 0;">-<span id="LC488" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># print("loop counter", loop_counter)</span></span>
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489
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<pre style="margin: 0;">-<span id="LC489" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># print("nstart", nstart)</span></span>
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<pre style="margin: 0;">-<span id="LC490" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># print("nend", nend)</span></span>
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511
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="cython"> <span class="n" style="color: #333;">nhit</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nhits</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">]</span></span>
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512
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="cython"> <span class="n" style="color: #333;">nstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">starts</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">]</span></span>
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513
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<pre style="margin: 0;">+<span id="LC513" class="line" lang="cython"> <span class="n" style="color: #333;">nend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ends</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">]</span></span>
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491
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514
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<pre style="margin: 0;"> <span id="LC514" class="line" lang="cython"></span>
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492
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<pre style="margin: 0;">-<span id="LC492" class="line" lang="cython"> <span class="n" style="color: #333;">cn</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">find_intervals</span><span class="p">(</span><span class="n" style="color: #333;">it</span><span class="p">,</span> <span class="n" style="color: #333;">nstart</span><span class="p">,</span> <span class="n" style="color: #333;">nend</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">im</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">ntop</span><span class="p">,</span></span>
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515
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="cython"> <span class="k" style="font-weight: 600;">while</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 class="p">:</span></span>
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516
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="cython"> <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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517
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="cython"> <span class="n" style="color: #333;">cn</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">find_intervals</span><span class="p">(</span><span class="n" style="color: #333;">it</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">starts</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">],</span> <span class="kt" style="color: #458; font-weight: 600;">ends</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">],</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">im</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">ntop</span><span class="p">,</span></span>
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493
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<td class="new_line diff-line-num" data-linenumber="518" 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">
518
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<pre style="margin: 0;"> <span id="LC518" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">subheader</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">nlists</span><span class="p">,</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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494
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<pre style="margin: 0;">-<span id="LC494" class="line" lang="cython"> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">nhit</span><span class="p">),</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">it</span><span class="p">))</span> <span class="c1" style="color: #998; font-style: italic;"># GET NEXT BUFFER CHUNK</span></span>
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495
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<pre style="margin: 0;">-<span id="LC495" class="line" lang="cython"></span>
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496
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<pre style="margin: 0;">-<span id="LC496" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;">#print("nhits:", nhit)</span></span>
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497
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<pre style="margin: 0;">-<span id="LC497" class="line" lang="cython"></span>
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498
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<pre style="margin: 0;">-<span id="LC498" class="line" lang="cython"></span>
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519
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="cython"> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">na</span><span class="p">),</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">it</span><span class="p">))</span> <span class="c1" style="color: #998; font-style: italic;"># GET NEXT BUFFER CHUNK</span></span>
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499
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520
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<pre style="margin: 0;"> <span id="LC520" class="line" lang="cython"></span>
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500
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521
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<pre style="margin: 0;"> <span id="LC521" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">nfound</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">nhit</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">length</span><span class="p">:</span></span>
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501
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<pre style="margin: 0;">-<span id="LC501" class="line" lang="cython"></span>
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502
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<td class="new_line diff-line-num old" data-linenumber="522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC502" class="line" lang="cython"> <span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">nfound</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">nhit</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span></span>
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522
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="cython"> <span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">nhit</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span></span>
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503
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523
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<pre style="margin: 0;"> <span id="LC523" 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;">resize</span><span class="p">(</span><span class="n" style="color: #333;">output_arr</span><span class="p">,</span> <span class="n" style="color: #333;">length</span><span class="p">)</span></span>
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504
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524
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<pre style="margin: 0;"> <span id="LC524" class="line" lang="cython"> <span class="n" style="color: #333;">output_arr_start</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;">resize</span><span class="p">(</span><span class="n" style="color: #333;">output_arr_start</span><span class="p">,</span> <span class="n" style="color: #333;">length</span><span class="p">)</span></span>
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505
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525
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<pre style="margin: 0;"> <span id="LC525" 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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="507" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="527" 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">@@ -507,9 +527,6 @@ cdef class NCLS32:</td>
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507
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527
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<pre style="margin: 0;"> <span id="LC527" class="line" lang="cython"> <span class="n" style="color: #333;">output_arr_end</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;">resize</span><span class="p">(</span><span class="n" style="color: #333;">output_arr_end</span><span class="p">,</span> <span class="n" style="color: #333;">length</span><span class="p">)</span></span>
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508
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528
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<pre style="margin: 0;"> <span id="LC528" class="line" lang="cython"> <span class="n" style="color: #333;">output_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">output_arr_end</span></span>
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509
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529
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<pre style="margin: 0;"> <span id="LC529" class="line" lang="cython"></span>
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510
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<pre style="margin: 0;">-<span id="LC510" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># print(" length is", length)</span></span>
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511
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<pre style="margin: 0;">-<span id="LC511" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># print(" nfound is", nfound)</span></span>
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512
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<pre style="margin: 0;">-<span id="LC512" class="line" lang="cython"></span>
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513
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530
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<pre style="margin: 0;"> <span id="LC530" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># B covers whole of A; ignore</span></span>
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514
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531
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<pre style="margin: 0;"> <span id="LC531" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">nhit</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">starts</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">im_buf</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">start</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">ends</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">im_buf</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">end</span><span class="p">:</span></span>
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515
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532
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<pre style="margin: 0;"> <span id="LC532" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># print("ignore me!")</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="518" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="535" 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">@@ -518,66 +535,46 @@ cdef class NCLS32:</td>
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518
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535
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<pre style="margin: 0;"> <span id="LC535" class="line" lang="cython"> <span class="n" style="color: #333;">output</span><span class="p">[</span><span class="n" style="color: #333;">nfound</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">indexes</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">]</span></span>
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519
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536
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<pre style="margin: 0;"> <span id="LC536" class="line" lang="cython"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nhit</span></span>
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537
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<pre style="margin: 0;"> <span id="LC537" class="line" lang="cython"> <span class="n" style="color: #333;">nfound</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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538
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<pre style="margin: 0;">+<span id="LC538" class="line" lang="cython"> <span class="k" style="font-weight: 600;">break</span></span>
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539
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<pre style="margin: 0;"> <span id="LC539" class="line" lang="cython"></span>
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522
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<pre style="margin: 0;">-<span id="LC522" class="line" lang="cython"> <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nhit</span><span class="p">:</span></span>
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523
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<pre style="margin: 0;">-<span id="LC523" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># print(" i", i)</span></span>
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524
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<pre style="margin: 0;">-<span id="LC524" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># print("--- i:", i)</span></span>
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525
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<pre style="margin: 0;">-<span id="LC525" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># print("--- im_buf[i]", im_buf[i])</span></span>
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526
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<pre style="margin: 0;">-<span id="LC526" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># print(" B start:", im_buf[i].start)</span></span>
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527
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<pre style="margin: 0;">-<span id="LC527" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># print(" B end:", im_buf[i].end)</span></span>
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528
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<pre style="margin: 0;">-<span id="LC528" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># print(" nfound:", nfound)</span></span>
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529
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<pre style="margin: 0;">-<span id="LC529" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># print(" output_arr_start", output_arr_start)</span></span>
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530
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<pre style="margin: 0;">-<span id="LC530" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># print(" output_arr_end", output_arr_end)</span></span>
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540
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<pre style="margin: 0;">+<span id="LC540" class="line" lang="cython"> <span class="n" style="color: #333;">max_i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1024</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">nhit</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1024</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">nhit</span></span>
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531
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541
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<pre style="margin: 0;"> <span id="LC541" class="line" lang="cython"></span>
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<td class="new_line diff-line-num new" data-linenumber="542" 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">
542
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<pre style="margin: 0;">+<span id="LC542" class="line" lang="cython"> <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">max_i</span><span class="p">:</span></span>
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532
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543
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<pre style="margin: 0;"> <span id="LC543" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># in case the start contributes nothing</span></span>
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533
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<pre style="margin: 0;">-<span id="LC533" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nhit</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>
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534
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<pre style="margin: 0;">-<span id="LC534" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># print(" i < nhit - 1")</span></span>
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544
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<pre style="margin: 0;">+<span id="LC544" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">nstart</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">im_buf</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">start</span><span class="p">:</span></span>
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545
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="cython"> <span class="n" style="color: #333;">output</span><span class="p">[</span><span class="n" style="color: #333;">nfound</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">indexes</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">]</span></span>
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546
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="cython"> <span class="n" style="color: #333;">output_start</span><span class="p">[</span><span class="n" style="color: #333;">nfound</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nstart</span></span>
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547
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<pre style="margin: 0;">+<span id="LC547" class="line" lang="cython"> <span class="n" style="color: #333;">output_end</span><span class="p">[</span><span class="n" style="color: #333;">nfound</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">im_buf</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">start</span></span>
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548
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<pre style="margin: 0;">+<span id="LC548" class="line" lang="cython"> <span class="n" style="color: #333;">nfound</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="cython"> <span class="n" style="color: #333;">nstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">im_buf</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">end</span></span>
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535
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<pre style="margin: 0;"> <span id="LC550" class="line" lang="cython"></span>
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536
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<pre style="margin: 0;">-<span id="LC536" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">nstart</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">im_buf</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">start</span><span class="p">:</span></span>
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537
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<pre style="margin: 0;">-<span id="LC537" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;">#print(" new_start", nstart)</span></span>
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538
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<pre style="margin: 0;">-<span id="LC538" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;">#print(" new_end", im_buf[i].start)</span></span>
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539
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<pre style="margin: 0;">-<span id="LC539" class="line" lang="cython"> <span class="n" style="color: #333;">output</span><span class="p">[</span><span class="n" style="color: #333;">nfound</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">indexes</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">]</span></span>
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540
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<pre style="margin: 0;">-<span id="LC540" class="line" lang="cython"> <span class="n" style="color: #333;">output_start</span><span class="p">[</span><span class="n" style="color: #333;">nfound</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nstart</span></span>
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541
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<pre style="margin: 0;">-<span id="LC541" class="line" lang="cython"> <span class="n" style="color: #333;">output_end</span><span class="p">[</span><span class="n" style="color: #333;">nfound</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">im_buf</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">start</span></span>
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542
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<pre style="margin: 0;">-<span id="LC542" class="line" lang="cython"> <span class="n" style="color: #333;">nfound</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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551
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<pre style="margin: 0;">+<span id="LC551" class="line" lang="cython"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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543
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552
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<pre style="margin: 0;"> <span id="LC552" class="line" lang="cython"></span>
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544
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<pre style="margin: 0;">-<span id="LC544" class="line" lang="cython"> <span class="n" style="color: #333;">nstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">im_buf</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">end</span></span>
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545
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<pre style="margin: 0;">-<span id="LC545" class="line" lang="cython"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">nhit</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>
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553
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<pre style="margin: 0;">+<span id="LC553" class="line" lang="cython"> <span class="n" style="color: #333;">nhit</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nhit</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1024</span></span>
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546
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554
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<pre style="margin: 0;"> <span id="LC554" class="line" lang="cython"></span>
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547
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<pre style="margin: 0;">-<span id="LC547" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># print("i == nhit -1")</span></span>
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548
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<pre style="margin: 0;">-<span id="LC548" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;">#print("im_buf[i].start", im_buf[i].start)</span></span>
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549
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<pre style="margin: 0;">-<span id="LC549" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;">#print("im_buf[i].end", im_buf[i].end)</span></span>
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550
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<pre style="margin: 0;">-<span id="LC550" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;">#print("nstart", nstart)</span></span>
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551
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<pre style="margin: 0;">-<span id="LC551" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;">#print("ends[loop_counter]", ends[loop_counter])</span></span>
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555
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<pre style="margin: 0;">+<span id="LC555" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</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 class="p">:</span></span>
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556
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<pre style="margin: 0;">+<span id="LC556" class="line" lang="cython"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span></span>
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552
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557
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<pre style="margin: 0;"> <span id="LC557" class="line" lang="cython"></span>
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553
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<pre style="margin: 0;">-<span id="LC553" class="line" lang="cython"> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">im_buf</span><span class="p">[</span><span class="n" style="color: #333;">i</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;">nstart</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">im_buf</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">ends</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">]:</span></span>
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554
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<pre style="margin: 0;">-<span id="LC554" class="line" lang="cython"> <span class="idiff left right"> </span><span class="c1" style="color: #998; font-style: italic;"># print("im_buf[i].start <= nstart and im_buf[i].end >= ends[loop_counter]")</span></span>
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555
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<pre style="margin: 0;">-<span id="LC555" class="line" lang="cython"> <span class="idiff left right"> </span><span class="c1" style="color: #998; font-style: italic;">#print("we are here " * 10)</span></span>
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<pre style="margin: 0;">+<span id="LC558" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">im_buf</span><span class="p">[</span><span class="n" style="color: #333;">i</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;">nstart</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">im_buf</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">ends</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">]:</span></span>
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559
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># print("im_buf[i].start <= nstart and im_buf[i].end >= ends[loop_counter]")</span></span>
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560
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<pre style="margin: 0;">+<span id="LC560" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;">#print("we are here " * 10)</span></span>
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556
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561
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<pre style="margin: 0;"> <span id="LC561" class="line" lang="cython"></span>
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557
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<td class="new_line diff-line-num old" data-linenumber="562" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC557" class="line" lang="cython"> <span class="n" style="color: #333;">output_start</span><span class="p">[</span><span class="n" style="color: #333;">nfound</span><span class="p">]</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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558
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<td class="new_line diff-line-num old" data-linenumber="562" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC558" class="line" lang="cython"> <span class="n" style="color: #333;">output_end</span><span class="p">[</span><span class="n" style="color: #333;">nfound</span><span class="p">]</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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<td class="new_line diff-line-num new" data-linenumber="562" 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">
562
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="cython"> <span class="n" style="color: #333;">output_start</span><span class="p">[</span><span class="n" style="color: #333;">nfound</span><span class="p">]</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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<td class="new_line diff-line-num new" data-linenumber="563" 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">
563
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<pre style="margin: 0;">+<span id="LC563" class="line" lang="cython"> <span class="n" style="color: #333;">output_end</span><span class="p">[</span><span class="n" style="color: #333;">nfound</span><span class="p">]</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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<td class="new_line diff-line-num new" data-linenumber="564" 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">
564
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<pre style="margin: 0;">+<span id="LC564" class="line" lang="cython"> <span class="n" style="color: #333;">output</span><span class="p">[</span><span class="n" style="color: #333;">nfound</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;"><</span><span class="nb" style="color: #0086b3;">long</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">indexes</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">]</span></span>
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565
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<pre style="margin: 0;">+<span id="LC565" class="line" lang="cython"> <span class="n" style="color: #333;">nfound</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="new_line diff-line-num new" data-linenumber="566" 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">
566
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="cython"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="567" 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">
567
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<pre style="margin: 0;">+<span id="LC567" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">im_buf</span><span class="p">[</span><span class="n" style="color: #333;">i</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;">nstart</span><span class="p">:</span></span>
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559
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<td class="new_line diff-line-num" data-linenumber="568" 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">
568
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<pre style="margin: 0;"> <span id="LC568" class="line" lang="cython"> <span class="n" style="color: #333;">output</span><span class="p">[</span><span class="n" style="color: #333;">nfound</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">indexes</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">]</span></span>
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569
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<pre style="margin: 0;">+<span id="LC569" class="line" lang="cython"> <span class="n" style="color: #333;">output_start</span><span class="p">[</span><span class="n" style="color: #333;">nfound</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nstart</span></span>
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570
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<pre style="margin: 0;">+<span id="LC570" class="line" lang="cython"> <span class="n" style="color: #333;">output_end</span><span class="p">[</span><span class="n" style="color: #333;">nfound</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">im_buf</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">start</span></span>
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560
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<td class="new_line diff-line-num" data-linenumber="571" 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">
571
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<pre style="margin: 0;"> <span id="LC571" class="line" lang="cython"> <span class="n" style="color: #333;">nfound</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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561
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<td class="new_line diff-line-num old" data-linenumber="572" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC561" class="line" lang="cython"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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562
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<td class="new_line diff-line-num old" data-linenumber="572" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC562" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">im_buf</span><span class="p">[</span><span class="n" style="color: #333;">i</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;">nstart</span><span class="p">:</span></span>
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563
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<td class="new_line diff-line-num old" data-linenumber="572" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC563" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># print("im_buf[i].start > nstart", im_buf[i].start, nstart)</span></span>
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564
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<td class="new_line diff-line-num old" data-linenumber="572" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC564" class="line" lang="cython"> <span class="n" style="color: #333;">output</span><span class="p">[</span><span class="n" style="color: #333;">nfound</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">indexes</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">]</span></span>
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565
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<td class="new_line diff-line-num old" data-linenumber="572" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC565" class="line" lang="cython"> <span class="n" style="color: #333;">output_start</span><span class="p">[</span><span class="n" style="color: #333;">nfound</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nstart</span></span>
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566
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<pre style="margin: 0;">-<span id="LC566" class="line" lang="cython"> <span class="n" style="color: #333;">output_end</span><span class="p">[</span><span class="n" style="color: #333;">nfound</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">im_buf</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">start</span></span>
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567
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<pre style="margin: 0;">-<span id="LC567" class="line" lang="cython"> <span class="n" style="color: #333;">nfound</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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568
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<pre style="margin: 0;">-<span id="LC568" class="line" lang="cython"></span>
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569
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<td class="new_line diff-line-num old" data-linenumber="572" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC569" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">im_buf</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">ends</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">]:</span></span>
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570
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<td class="new_line diff-line-num old" data-linenumber="572" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC570" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># print("im_buf[i].end < ends[loop_counter]", im_buf[i].end, ends[loop_counter])</span></span>
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571
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<td class="new_line diff-line-num old" data-linenumber="572" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC571" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># print("i, loop_counter", i, loop_counter)</span></span>
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572
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<pre style="margin: 0;">-<span id="LC572" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># print("indexes[loop_counter]", indexes[loop_counter])</span></span>
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573
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<pre style="margin: 0;">-<span id="LC573" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># print("indexes", indexes[loop_counte rloop_counter])</span></span>
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574
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<pre style="margin: 0;">-<span id="LC574" class="line" lang="cython"></span>
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575
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<pre style="margin: 0;">-<span id="LC575" class="line" lang="cython"> <span class="n" style="color: #333;">output</span><span class="p">[</span><span class="n" style="color: #333;">nfound</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">indexes</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">]</span></span>
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576
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<pre style="margin: 0;">-<span id="LC576" class="line" lang="cython"> <span class="n" style="color: #333;">output_start</span><span class="p">[</span><span class="n" style="color: #333;">nfound</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">im_buf</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">end</span></span>
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577
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<pre style="margin: 0;">-<span id="LC577" class="line" lang="cython"> <span class="n" style="color: #333;">output_end</span><span class="p">[</span><span class="n" style="color: #333;">nfound</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ends</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">]</span></span>
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578
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<pre style="margin: 0;">-<span id="LC578" class="line" lang="cython"> <span class="n" style="color: #333;">nfound</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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579
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572
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<pre style="margin: 0;"> <span id="LC572" class="line" lang="cython"></span>
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580
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<td class="new_line diff-line-num old" data-linenumber="573" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC580" class="line" lang="cython"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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573
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<pre style="margin: 0;">+<span id="LC573" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">im_buf</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">ends</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">]:</span></span>
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574
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<pre style="margin: 0;">+<span id="LC574" class="line" lang="cython"> <span class="n" style="color: #333;">output</span><span class="p">[</span><span class="n" style="color: #333;">nfound</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">indexes</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">]</span></span>
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575
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<pre style="margin: 0;">+<span id="LC575" class="line" lang="cython"> <span class="n" style="color: #333;">output_start</span><span class="p">[</span><span class="n" style="color: #333;">nfound</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">im_buf</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">end</span></span>
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576
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<pre style="margin: 0;">+<span id="LC576" class="line" lang="cython"> <span class="n" style="color: #333;">output_end</span><span class="p">[</span><span class="n" style="color: #333;">nfound</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ends</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">]</span></span>
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577
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<pre style="margin: 0;">+<span id="LC577" class="line" lang="cython"> <span class="n" style="color: #333;">nfound</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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578
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<pre style="margin: 0;"> <span id="LC578" class="line" lang="cython"></span>
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582
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579
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<pre style="margin: 0;"> <span id="LC579" class="line" lang="cython"> <span class="n" style="color: #333;">cn</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">reset_interval_iterator</span><span class="p">(</span><span class="n" style="color: #333;">it_alloc</span><span class="p">)</span></span>
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583
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580
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<pre style="margin: 0;"> <span id="LC580" class="line" lang="cython"> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">it_alloc</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">@@ -639,6 +636,7 @@ cdef class NCLS32:</td>
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639
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636
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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;">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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640
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637
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<pre style="margin: 0;"> <span id="LC637" 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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641
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638
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<pre style="margin: 0;"> <span id="LC638" 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;">start</span><span class="p">,</span> <span class="n" style="color: #333;">end</span></span>
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639
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<pre style="margin: 0;">+<span id="LC639" 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;">spent</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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642
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640
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<pre style="margin: 0;"> <span id="LC640" class="line" lang="cython"></span>
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641
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<pre style="margin: 0;"> <span id="LC641" 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;">long</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC642" 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;">long</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="662" 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">@@ -664,7 +662,8 @@ cdef class NCLS32:</td>
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664
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662
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<pre style="margin: 0;"> <span id="LC662" class="line" lang="cython"></span>
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<pre style="margin: 0;"> <span id="LC663" class="line" lang="cython"> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">starts</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">]</span></span>
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666
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<pre style="margin: 0;"> <span id="LC664" class="line" lang="cython"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ends</span><span class="p">[</span><span class="n" style="color: #333;">loop_counter</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC667" class="line" lang="cython"> <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">it</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC665" class="line" lang="cython"> <span class="n" style="color: #333;">spent</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;">+<span id="LC666" class="line" lang="cython"> <span class="k" style="font-weight: 600;">while</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">spent</span><span class="p">:</span></span>
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667
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<pre style="margin: 0;"> <span id="LC667" class="line" lang="cython"> <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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668
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<pre style="margin: 0;"> <span id="LC668" class="line" lang="cython"> <span class="n" style="color: #333;">cn</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">find_intervals</span><span class="p">(</span><span class="n" style="color: #333;">it</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="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">im</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">ntop</span><span class="p">,</span></span>
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669
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<pre style="margin: 0;"> <span id="LC669" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">subheader</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">nlists</span><span class="p">,</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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="688" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="687" 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">@@ -688,6 +687,9 @@ cdef class NCLS32:</td>
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<pre style="margin: 0;"> <span id="LC687" class="line" lang="cython"> <span class="n" style="color: #333;">nfound</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;"> <span id="LC688" class="line" lang="cython"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;"> <span id="LC689" class="line" lang="cython"></span>
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<pre style="margin: 0;">+<span id="LC690" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">nhit</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1024</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC691" class="line" lang="cython"> <span class="n" style="color: #333;">spent</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">+<span id="LC692" class="line" lang="cython"></span>
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<pre style="margin: 0;"> <span id="LC693" class="line" lang="cython"> <span class="n" style="color: #333;">cn</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">reset_interval_iterator</span><span class="p">(</span><span class="n" style="color: #333;">it_alloc</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC694" class="line" lang="cython"> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">it_alloc</span></span>
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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.<span class="idiff left right">57</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.<span class="idiff left right">63</span>"</span></span></pre>
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