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<h3>
Steffen Möller pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/python-bx">Debian Med / python-bx</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-bx/commit/f480150128258ed3a2c2602d742e1f18de23101c">f4801501</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2019-11-08T18:11:30Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.8.5</pre>
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<h4>3 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#62905aa149135a3639dcfd6a51e2193f4b890028">
lib/bx/bbi/bigwig_file.pyx
</a>
</li>
<li class="file-stats">
<a href="#0a89409d04b7f18042928eb97a444e22750e9409">
lib/bx/bbi/bpt_file.pyx
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</li>
<li class="file-stats">
<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
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<h4>Changes:</h4>
<li id="62905aa149135a3639dcfd6a51e2193f4b890028">
<a href="https://salsa.debian.org/med-team/python-bx/commit/f480150128258ed3a2c2602d742e1f18de23101c#62905aa149135a3639dcfd6a51e2193f4b890028"><strong>lib/bx/bbi/bigwig_file.pyx</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -123,7 +123,37 @@ cdef class ArrayAccumulatingBlockHandler( BigWigBlockHandler ):</td>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="cython"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="k" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">-</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start</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="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;">-</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="cython"> <span class="kt" style="color: #458; font-weight: 600;">array</span><span class="p">[</span> <span class="n" style="color: #333;">i</span> <span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">val</span></span>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="cython"></span>
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="cython"><span class="k" style="font-weight: 600;">cdef</span> <span class="kr" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">BigWigFile</span><span class="p">(</span> <span class="n" style="color: #333;">BBIFile</span> <span class="p">):</span> </span>
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<td class="diff-line-num new new_line" data-linenumber="126" 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="LC126" class="line" lang="cython"><span class="k" style="font-weight: 600;">cdef</span> <span class="kr" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">BigWigHeaderBlockHandler</span><span class="p">(</span> <span class="n" style="color: #333;">BigWigBlockHandler</span> <span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="cython"> <span class="s" style="color: #d14;">"Reads and returns headers"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="128" 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="LC128" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">list</span> <span class="n" style="color: #333;">headers</span></span>
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<td class="diff-line-num new new_line" data-linenumber="129" 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="LC129" class="line" lang="cython"></span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="cython"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</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;">bits32</span> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bits32</span> <span class="n" style="color: #333;">end</span> <span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="cython"> <span class="n" style="color: #333;">BigWigBlockHandler</span><span class="o" style="font-weight: 600;">.</span><span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span> <span class="bp" style="color: #999;">self</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>
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<td class="diff-line-num new new_line" data-linenumber="132" 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="LC132" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">headers</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="133" 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="LC133" class="line" lang="cython"></span>
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<td class="diff-line-num new new_line" data-linenumber="134" 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="LC134" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="nf" style="color: #900; font-weight: 600;">handle_block</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;">bytes</span> <span class="n" style="color: #333;">block_data</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">BBIFile</span> <span class="n" style="color: #333;">bbi_file</span> <span class="p">):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="135" 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">
135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">bits32</span> <span class="n" style="color: #333;">b_chrom_id</span><span class="p">,</span> <span class="n" style="color: #333;">b_start</span><span class="p">,</span> <span class="n" style="color: #333;">b_end</span><span class="p">,</span> <span class="n" style="color: #333;">b_valid_count</span></span>
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<td class="diff-line-num new new_line" data-linenumber="136" 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">
136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">bits32</span> <span class="n" style="color: #333;">b_item_step</span><span class="p">,</span> <span class="n" style="color: #333;">b_item_span</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">bits16</span> <span class="n" style="color: #333;">b_item_count</span></span>
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">UBYTE</span> <span class="n" style="color: #333;">b_type</span></span>
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<pre style="margin: 0;">+<span id="LC139" 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;">s</span><span class="p">,</span> <span class="n" style="color: #333;">e</span></span>
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<td class="diff-line-num new new_line" data-linenumber="140" 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">
140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">val</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># parse the block header</span></span>
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<td class="diff-line-num new new_line" data-linenumber="142" 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">
142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="cython"> <span class="n" style="color: #333;">block_reader</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">BinaryFileReader</span><span class="p">(</span> <span class="nf" style="color: #900; font-weight: 600;">BytesIO</span><span class="p">(</span> <span class="n" style="color: #333;">block_data</span> <span class="p">),</span> <span class="n" style="color: #333;">is_little_endian</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">bbi_file</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reader</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">is_little_endian</span> <span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="143" 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">
143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="cython"> <span class="n" style="color: #333;">b_chrom_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">block_reader</span><span class="o" style="font-weight: 600;">.</span><span class="nf" style="color: #900; font-weight: 600;">read_uint32</span><span class="p">()</span></span>
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<td class="diff-line-num new new_line" data-linenumber="144" 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">
144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="cython"> <span class="n" style="color: #333;">b_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">block_reader</span><span class="o" style="font-weight: 600;">.</span><span class="nf" style="color: #900; font-weight: 600;">read_uint32</span><span class="p">()</span></span>
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<td class="diff-line-num new new_line" data-linenumber="145" 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">
145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="cython"> <span class="n" style="color: #333;">b_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">block_reader</span><span class="o" style="font-weight: 600;">.</span><span class="nf" style="color: #900; font-weight: 600;">read_uint32</span><span class="p">()</span></span>
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<td class="diff-line-num new new_line" data-linenumber="146" 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">
146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="cython"> <span class="n" style="color: #333;">b_item_step</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">block_reader</span><span class="o" style="font-weight: 600;">.</span><span class="nf" style="color: #900; font-weight: 600;">read_uint32</span><span class="p">()</span></span>
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<td class="diff-line-num new new_line" data-linenumber="147" 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">
147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="cython"> <span class="n" style="color: #333;">b_item_span</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">block_reader</span><span class="o" style="font-weight: 600;">.</span><span class="nf" style="color: #900; font-weight: 600;">read_uint32</span><span class="p">()</span></span>
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<td class="diff-line-num new new_line" data-linenumber="148" 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">
148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="cython"> <span class="n" style="color: #333;">b_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">block_reader</span><span class="o" style="font-weight: 600;">.</span><span class="nf" style="color: #900; font-weight: 600;">read_uint8</span><span class="p">()</span></span>
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<td class="diff-line-num new new_line" data-linenumber="149" 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">
149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="cython"> <span class="n" style="color: #333;">block_reader</span><span class="o" style="font-weight: 600;">.</span><span class="nf" style="color: #900; font-weight: 600;">skip</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="cython"> <span class="n" style="color: #333;">b_item_count</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">block_reader</span><span class="o" style="font-weight: 600;">.</span><span class="nf" style="color: #900; font-weight: 600;">read_uint16</span><span class="p">()</span></span>
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<td class="diff-line-num new new_line" data-linenumber="151" 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">
151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nf" style="color: #900; font-weight: 600;">handle_header</span><span class="p">(</span> <span class="n" style="color: #333;">b_start</span><span class="p">,</span> <span class="n" style="color: #333;">b_end</span><span class="p">,</span> <span class="n" style="color: #333;">b_item_step</span><span class="p">,</span> <span class="n" style="color: #333;">b_item_span</span><span class="p">,</span> <span class="n" style="color: #333;">b_type</span><span class="p">,</span> <span class="n" style="color: #333;">b_item_count</span> <span class="p">)</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="cython"></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="nf" style="color: #900; font-weight: 600;">handle_header</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;">bits32</span> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bits32</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bits32</span> <span class="n" style="color: #333;">step</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bits32</span> <span class="n" style="color: #333;">span</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bits8</span> <span class="nb" style="color: #0086b3;">type</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bits16</span> <span class="n" style="color: #333;">itemCount</span> <span class="p">):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="154" 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">
154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">headers</span><span class="o" style="font-weight: 600;">.</span><span class="nf" style="color: #900; font-weight: 600;">append</span><span class="p">(</span> <span class="p">(</span> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">step</span><span class="p">,</span> <span class="n" style="color: #333;">span</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="p">,</span> <span class="n" style="color: #333;">itemCount</span> <span class="p">)</span> <span class="p">)</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="cython"></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="cython"><span class="k" style="font-weight: 600;">cdef</span> <span class="kr" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">BigWigFile</span><span class="p">(</span> <span class="n" style="color: #333;">BBIFile</span> <span class="p">):</span></span>
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127
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157
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="cython"> <span class="s" style="color: #d14;">"""</span></span>
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128
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158
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="cython"><span class="s" style="color: #d14;"> A "big binary indexed" file whose raw data is in wiggle format.</span></span>
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129
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159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="cython"><span class="s" style="color: #d14;"> """</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="140" 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="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">@@ -140,7 +170,7 @@ cdef class BigWigFile( BBIFile ):</td>
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140
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170
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="cython"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="k" style="font-weight: 600;">from</span> <span class="mi" style="color: #099;">0</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="n" style="color: #333;">summary_size</span><span class="p">:</span></span>
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141
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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;">v</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">valid_count</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">round</span><span class="p">(</span> <span class="n" style="color: #333;">v</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">valid_count</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="p">)</span></span>
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142
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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;">return</span> <span class="n" style="color: #333;">v</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sd</span></span>
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143
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="cython"><span class="idiff left right"> </span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="cython"></span>
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144
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174
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cpdef</span> <span class="nf" style="color: #900; font-weight: 600;">get</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">chrom</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bits32</span> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bits32</span> <span class="n" style="color: #333;">end</span> <span class="p">):</span></span>
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145
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175
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="cython"> <span class="s" style="color: #d14;">"""</span></span>
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146
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176
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="cython"><span class="s" style="color: #d14;"> Gets all data points over the regions `chrom`:`start`-`end`.</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="167" 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="197" 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">@@ -167,6 +197,15 @@ cdef class BigWigFile( BBIFile ):</td>
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167
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197
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nf" style="color: #900; font-weight: 600;">visit_blocks_in_region</span><span class="p">(</span> <span class="n" style="color: #333;">chrom_id</span><span class="p">,</span> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">v</span> <span class="p">)</span></span>
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168
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198
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="cython"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">v</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">array</span></span>
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169
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199
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="cython"></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cpdef</span> <span class="nf" style="color: #900; font-weight: 600;">get_headers</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">chrom</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bits32</span> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bits32</span> <span class="n" style="color: #333;">end</span> <span class="p">):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="201" 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">
201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">end</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="202" 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">
202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="cython"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">None</span></span>
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<td class="diff-line-num new new_line" data-linenumber="203" 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">
203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="cython"> <span class="n" style="color: #333;">chrom_id</span><span class="p">,</span> <span class="n" style="color: #333;">chrom_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nf" style="color: #900; font-weight: 600;">_get_chrom_id_and_size</span><span class="p">(</span> <span class="n" style="color: #333;">chrom</span> <span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="204" 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">
204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">chrom_id</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="205" 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">
205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="cython"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">None</span></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="cython"> <span class="n" style="color: #333;">v</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">BigWigHeaderBlockHandler</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>
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nf" style="color: #900; font-weight: 600;">visit_blocks_in_region</span><span class="p">(</span> <span class="n" style="color: #333;">chrom_id</span><span class="p">,</span> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">v</span> <span class="p">)</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="cython"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">v</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">headers</span></span>
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170
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209
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="cython"></span>
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210
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="cython"></span>
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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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<a href="https://salsa.debian.org/med-team/python-bx/commit/f480150128258ed3a2c2602d742e1f18de23101c#0a89409d04b7f18042928eb97a444e22750e9409"><strong>lib/bx/bbi/bpt_file.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">@@ -10,26 +10,26 @@ cdef class BPTFile:</td>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="cython"><span class="s" style="color: #d14;"> On disk B+ tree compatible with Jim Kent's bPlusTree.c</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="cython"><span class="s" style="color: #d14;"> """</span></span>
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="cython"></span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="cython"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">file</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff">None</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="cython"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">file</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">None</span></span><span class="p">):</span></span>
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14
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">file</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nf" style="color: #900; font-weight: 600;">attach</span><span class="p">(</span><span class="idiff left"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">file</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nf" style="color: #900; font-weight: 600;">attach</span><span class="p">(</span><span class="nb" style="color: #0086b3;"><span class="idiff left right">file</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="cython"></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="cython"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">attach</span><span class="p">(</span><span class="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">file</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="cython"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">attach</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">file</span></span><span class="p">):</span></span>
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="cython"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="cython"><span class="s" style="color: #d14;"> Attach to an open file</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="cython"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">file</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">file</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reader</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">reader</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">BinaryFileReader</span><span class="p">(</span><span class="idiff left"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">file</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">bpt_sig</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reader</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">reader</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">BinaryFileReader</span><span class="p">(</span><span class="nb" style="color: #0086b3;"><span class="idiff left">file</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">bpt_sig</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">is_byteswapped</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reader</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">byteswap_needed</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># Read header stuff</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">block_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">reader</span><span class="o" style="font-weight: 600;">.</span><span class="nf" style="color: #900; font-weight: 600;">read_uint32</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">key_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">reader</span><span class="o" style="font-weight: 600;">.</span><span class="nf" style="color: #900; font-weight: 600;">read_uint32</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">value_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">reader</span><span class="o" style="font-weight: 600;">.</span><span class="nf" style="color: #900; font-weight: 600;">read_uint32</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">item_count</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">reader</span><span class="o" style="font-weight: 600;">.</span><span class="nf" style="color: #900; font-weight: 600;">read_uint64</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="cython"> <span class="n" style="color: #333;">reader</span><span class="o" style="font-weight: 600;">.</span><span class="nf" style="color: #900; font-weight: 600;">skip</span><span class="p">(</span><span class="idiff left"> </span><span class="mi" style="color: #099;"><span class="idiff">8</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="cython"> <span class="n" style="color: #333;">reader</span><span class="o" style="font-weight: 600;">.</span><span class="nf" style="color: #900; font-weight: 600;">skip</span><span class="p">(</span><span class="mi" style="color: #099;"><span class="idiff left right">8</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">root_offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">reader</span><span class="o" style="font-weight: 600;">.</span><span class="nf" style="color: #900; font-weight: 600;">tell</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="cython"></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="cython"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">r_find</span><span class="p">(</span><span class="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">bits64</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">block_start</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">key</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="cython"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">r_find</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">bits64</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">block_start</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">key</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="cython"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="cython"><span class="s" style="color: #d14;"> Recursively seek the value matching key under the subtree starting</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="cython"><span class="s" style="color: #d14;"> at file offset `block_start`</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -37,31 +37,31 @@ cdef class BPTFile:</td>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">UBYTE</span> <span class="n" style="color: #333;">is_leaf</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">bits16</span> <span class="n" style="color: #333;">child_count</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">bits64</span> <span class="n" style="color: #333;">offset</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reader</span><span class="o" style="font-weight: 600;">.</span><span class="nf" style="color: #900; font-weight: 600;">seek</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">block_start</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reader</span><span class="o" style="font-weight: 600;">.</span><span class="nf" style="color: #900; font-weight: 600;">seek</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">block_start</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># Block header</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="cython"> <span class="n" style="color: #333;">is_leaf</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reader</span><span class="o" style="font-weight: 600;">.</span><span class="nf" style="color: #900; font-weight: 600;">read_uint8</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reader</span><span class="o" style="font-weight: 600;">.</span><span class="nf" style="color: #900; font-weight: 600;">read_uint8</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="cython"> <span class="n" style="color: #333;">child_count</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reader</span><span class="o" style="font-weight: 600;">.</span><span class="nf" style="color: #900; font-weight: 600;">read_uint16</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">is_leaf</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="cython"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="k" style="font-weight: 600;">from</span> <span class="mi" style="color: #099;">0</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="n" style="color: #333;">child_count</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="cython"> <span class="n" style="color: #333;">node_key</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reader</span><span class="o" style="font-weight: 600;">.</span><span class="nf" style="color: #900; font-weight: 600;">read</span><span class="p">(</span><span class="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">key_size</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="cython"> <span class="n" style="color: #333;">node_value</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reader</span><span class="o" style="font-weight: 600;">.</span><span class="nf" style="color: #900; font-weight: 600;">read</span><span class="p">(</span><span class="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">value_size</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="cython"> <span class="n" style="color: #333;">node_key</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reader</span><span class="o" style="font-weight: 600;">.</span><span class="nf" style="color: #900; font-weight: 600;">read</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">key_size</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="cython"> <span class="n" style="color: #333;">node_value</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reader</span><span class="o" style="font-weight: 600;">.</span><span class="nf" style="color: #900; font-weight: 600;">read</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">value_size</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">node_key</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">key</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="cython"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">node_value</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="cython"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="cython"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># Read and discard first key, store offset</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reader</span><span class="o" style="font-weight: 600;">.</span><span class="nf" style="color: #900; font-weight: 600;">read</span><span class="p">(</span><span class="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">key_size</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reader</span><span class="o" style="font-weight: 600;">.</span><span class="nf" style="color: #900; font-weight: 600;">read</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">key_size</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="cython"> <span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reader</span><span class="o" style="font-weight: 600;">.</span><span class="nf" style="color: #900; font-weight: 600;">read_uint64</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># Loop until correct subtree is found</span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="cython"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="k" style="font-weight: 600;">from</span> <span class="mi" style="color: #099;">0</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="n" style="color: #333;">child_count</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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58
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="cython"> <span class="n" style="color: #333;">node_key</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reader</span><span class="o" style="font-weight: 600;">.</span><span class="nf" style="color: #900; font-weight: 600;">read</span><span class="p">(</span><span class="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">key_size</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="cython"> <span class="n" style="color: #333;">node_key</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reader</span><span class="o" style="font-weight: 600;">.</span><span class="nf" style="color: #900; font-weight: 600;">read</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">key_size</span></span><span class="p">)</span></span>
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59
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">node_key</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">key</span><span class="p">:</span></span>
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60
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60
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="cython"> <span class="k" style="font-weight: 600;">break</span></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="cython"> <span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reader</span><span class="o" style="font-weight: 600;">.</span><span class="nf" style="color: #900; font-weight: 600;">read_uint64</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="cython"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nf" style="color: #900; font-weight: 600;">r_find</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">offset</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">key</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="cython"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nf" style="color: #900; font-weight: 600;">r_find</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">offset</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">key</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="cython"></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="cython"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">find</span><span class="p">(</span><span class="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">key</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="cython"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">find</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">key</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="cython"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="cython"><span class="s" style="color: #d14;"> Find the value matching `key` (a bytestring). Returns the matching</span></span>
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67
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="cython"><span class="s" style="color: #d14;"> value as a bytestring if found, or None</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="71" 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="71" 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">@@ -71,6 +71,6 @@ cdef class BPTFile:</td>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="cython"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># Key is less than key_size, right pad with 0 bytes</span></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">key</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">key_size</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="cython"> <span class="n" style="color: #333;">key</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p"><span class="idiff left">(</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'</span></span><span class="se" style="color: #d14;"><span class="idiff">\0</span></span><span class="s" style="color: #d14;"><span class="idiff">'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">key_size</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">len</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">key</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="cython"> <span class="n" style="color: #333;">key</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;"><span class="idiff left">b</span></span><span class="s" style="color: #d14;"><span class="idiff">'</span></span><span class="se" style="color: #d14;"><span class="idiff">\0</span></span><span class="s" style="color: #d14;"><span class="idiff">'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">key_size</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">len</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">key</span></span><span class="p"><span class="idiff right">)</span>)</span></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># Call the recursive finder</span></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="cython"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nf" style="color: #900; font-weight: 600;">r_find</span><span class="p">(</span><span class="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">root_offset</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">key</span></span><span class="idiff right"> </span><span class="p">)</span></span></pre>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="cython"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nf" style="color: #900; font-weight: 600;">r_find</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">root_offset</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">key</span></span><span class="p">)</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-bx/commit/f480150128258ed3a2c2602d742e1f18de23101c#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">platform</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">distutils.core</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Command</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">glob</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">glob</span></span>
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">version_info</span> <span class="o" style="font-weight: 600;"><</span> <span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">6</span><span class="p">):</span></span>
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5
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="s" style="color: #d14;">"ERROR: bx-python requires Python 2.6 or greater"</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="14" 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">@@ -12,57 +14,56 @@ except ImportError:</td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">ez_setup</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">use_setuptools</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"> <span class="n" style="color: #333;">use_setuptools</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">setuptools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="o" style="font-weight: 600;"><span class="idiff left right">*</span></span></span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;"><span class="idiff left">from</span></span><span class="idiff"> </span><span class="nn" style="color: #555;"><span class="idiff">glob</span></span><span class="idiff"> </span><span class="kn" style="font-weight: 600;"><span class="idiff">import</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">glob</span></span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">setuptools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;"><span class="idiff left">Extension</span></span><span class="idiff"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right"># noqa: E402</span></span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">():</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="python"> <span class="n" style="color: #333;">metadata</span> <span class="o" style="font-weight: 600;">=</span> \</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="python"> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"bx-python"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC22" 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;">"0.8.4"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="python"> <span class="n" style="color: #333;">setup_requires</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'numpy'</span><span class="p">,</span> <span class="s" style="color: #d14;">'cython'</span><span class="p">],</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="python"> <span class="n" style="color: #333;">install_requires</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'numpy'</span><span class="p">,</span> <span class="s" style="color: #d14;">'six'</span><span class="p">],</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="python"> <span class="n" style="color: #333;">py_modules</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span> <span class="s" style="color: #d14;">'psyco_full'</span> <span class="p">],</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">package_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span> <span class="s" style="color: #d14;">''</span><span class="p">:</span> <span class="s" style="color: #d14;">'lib'</span> <span class="p">},</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">package_data</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span> <span class="s" style="color: #d14;">''</span><span class="p">:</span> <span class="p">[</span><span class="s" style="color: #d14;">'*.ps'</span><span class="p">]</span> <span class="p">},</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">scripts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">glob</span><span class="p">(</span> <span class="s" style="color: #d14;">"scripts/*.py"</span> <span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="python"> <span class="n" style="color: #333;">test_suite</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'nose.collector'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="python"> <span class="n" style="color: #333;">tests_require</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'nose'</span><span class="p">,</span><span class="s" style="color: #d14;">'python-lzo'</span><span class="p">],</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="python"> <span class="n" style="color: #333;">author</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"James Taylor, Bob Harris, David King, Brent Pedersen, Kanwei Li, and others"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="python"> <span class="n" style="color: #333;">author_email</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"james@jamestaylor.org"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="python"> <span class="n" style="color: #333;">description</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Tools for manipulating biological data, particularly multiple sequence alignments"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="python"> <span class="n" style="color: #333;">url</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"https://github.com/bxlab/bx-python"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="python"> <span class="n" style="color: #333;">license</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"MIT"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="python"> <span class="n" style="color: #333;">classifiers</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="python"> <span class="s" style="color: #d14;">"Development Status :: 5 - Production/Stable"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="python"> <span class="s" style="color: #d14;">"Intended Audience :: Developers"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="python"> <span class="s" style="color: #d14;">"Intended Audience :: Science/Research"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="python"> <span class="s" style="color: #d14;">"License :: OSI Approved :: MIT License"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="python"> <span class="s" style="color: #d14;">"Operating System :: POSIX"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="python"> <span class="s" style="color: #d14;">"Programming Language :: Python :: 2"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="python"> <span class="s" style="color: #d14;">"Programming Language :: Python :: 2.6"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="python"> <span class="s" style="color: #d14;">"Programming Language :: Python :: 3"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="python"> <span class="s" style="color: #d14;">"Topic :: Scientific/Engineering :: Bio-Informatics"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="python"> <span class="s" style="color: #d14;">"Topic :: Software Development :: Libraries :: Python Modules"</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="python"> <span class="p">],</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="python"> <span class="n" style="color: #333;">zip_safe</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="python"> <span class="n" style="color: #333;">dependency_links</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[],</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="python"> <span class="n" style="color: #333;">cmdclass</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">command_classes</span> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"> <span class="n" style="color: #333;">metadata</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"bx-python"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC24" 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;">"0.8.5"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="n" style="color: #333;">setup_requires</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'numpy'</span><span class="p">,</span> <span class="s" style="color: #d14;">'cython'</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">install_requires</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'numpy'</span><span class="p">,</span> <span class="s" style="color: #d14;">'six'</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">py_modules</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'psyco_full'</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">package_dir</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span><span class="s" style="color: #d14;">''</span><span class="p">:</span> <span class="s" style="color: #d14;">'lib'</span><span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"> <span class="n" style="color: #333;">package_data</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span><span class="s" style="color: #d14;">''</span><span class="p">:</span> <span class="p">[</span><span class="s" style="color: #d14;">'*.ps'</span><span class="p">]},</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="n" style="color: #333;">scripts</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">glob</span><span class="p">(</span><span class="s" style="color: #d14;">"scripts/*.py"</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"> <span class="n" style="color: #333;">test_suite</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'nose.collector'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="n" style="color: #333;">tests_require</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'nose'</span><span class="p">,</span> <span class="s" style="color: #d14;">'python-lzo'</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"> <span class="n" style="color: #333;">author</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"James Taylor, Bob Harris, David King, Brent Pedersen, Kanwei Li, and others"</span><span class="p">,</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"> <span class="n" style="color: #333;">author_email</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"james@jamestaylor.org"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Tools for manipulating biological data, particularly multiple sequence alignments"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"> <span class="n" style="color: #333;">url</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"https://github.com/bxlab/bx-python"</span><span class="p">,</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"> <span class="n" style="color: #333;">license</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"MIT"</span><span class="p">,</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="n" style="color: #333;">classifiers</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="s" style="color: #d14;">"Development Status :: 5 - Production/Stable"</span><span class="p">,</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="s" style="color: #d14;">"Intended Audience :: Developers"</span><span class="p">,</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"> <span class="s" style="color: #d14;">"Intended Audience :: Science/Research"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> <span class="s" style="color: #d14;">"License :: OSI Approved :: MIT License"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"> <span class="s" style="color: #d14;">"Operating System :: POSIX"</span><span class="p">,</span></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="s" style="color: #d14;">"Programming Language :: Python :: 2"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"> <span class="s" style="color: #d14;">"Programming Language :: Python :: 2.7"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"> <span class="s" style="color: #d14;">"Programming Language :: Python :: 3"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"> <span class="s" style="color: #d14;">"Programming Language :: Python :: 3.5"</span><span class="p">,</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"> <span class="s" style="color: #d14;">"Programming Language :: Python :: 3.6"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="s" style="color: #d14;">"Programming Language :: Python :: 3.7"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="s" style="color: #d14;">"Programming Language :: Python :: 3.8"</span><span class="p">,</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="s" style="color: #d14;">"Topic :: Scientific/Engineering :: Bio-Informatics"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="s" style="color: #d14;">"Topic :: Software Development :: Libraries :: Python Modules"</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"> <span class="n" style="color: #333;">zip_safe</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="n" style="color: #333;">dependency_links</span><span class="o" style="font-weight: 600;">=</span><span class="p">[],</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"> <span class="n" style="color: #333;">cmdclass</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">command_classes</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="python"> <span class="n" style="color: #333;">numpy</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">numpy</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Suppress numpy tests</span></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="python"> <span class="n" style="color: #333;">numpy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">test</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span><span class="idiff left"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">Exception</span></span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="python"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">argv</span><span class="p">)</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">2</span> <span class="ow" style="font-weight: 600;">and</span> <span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'--help'</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sys</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">argv</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">:]</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff right">or</span></span></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="s" style="color: #d14;">'--help-commands'</span><span class="p">,</span> <span class="s" style="color: #d14;">'egg_info'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--version'</span><span class="p">,</span> <span class="s" style="color: #d14;">'clean'</span><span class="p">)):</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">argv</span><span class="p">)</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">2</span> <span class="ow" style="font-weight: 600;">and</span> <span class="idiff left right">\</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"> <span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'--help'</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sys</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">argv</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">:]</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">or</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="s" style="color: #d14;">'--help-commands'</span><span class="p">,</span> <span class="s" style="color: #d14;">'egg_info'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--version'</span><span class="p">,</span> <span class="s" style="color: #d14;">'clean'</span><span class="p">)):</span></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># For these actions, NumPy is not required.</span></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># They are required to succeed without Numpy for example when</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">@@ -71,23 +72,21 @@ def main():</td>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;"> <span id="LC73" 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="LC74" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">numpy</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC74" 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="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"numpy must be installed to build"</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="python"> <span class="n" style="color: #333;">metadata</span><span class="p">[</span><span class="s" style="color: #d14;">'packages'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">find_packages</span><span class="p">(</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">'lib'</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="python"> <span class="n" style="color: #333;">metadata</span><span class="p">[</span><span class="s" style="color: #d14;">'ext_modules'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_extension_modules</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">numpy_include</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">numpy</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">get_include</span></span><span class="p"><span class="idiff">()</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC75" 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;"><span class="idiff left right">"numpy must be installed to build"</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"> <span class="n" style="color: #333;">metadata</span><span class="p">[</span><span class="s" style="color: #d14;">'packages'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">find_packages</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left right">'lib'</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"> <span class="n" style="color: #333;">metadata</span><span class="p">[</span><span class="s" style="color: #d14;">'ext_modules'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_extension_modules</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">numpy_include</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">numpy</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">get_include</span></span><span class="p"><span class="idiff right">()</span>)</span></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="python"> <span class="n" style="color: #333;">setup</span><span class="p">(</span><span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">metadata</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ---- Commands -------------------------------------------------------------</span></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">distutils.core</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Command</span></span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Use build_ext from Cython if found</span></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="python"><span class="n" style="color: #333;">command_classes</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="python"><span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">Cython.Distutils</span></span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="python"> <span class="n" style="color: #333;">command_classes</span><span class="p">[</span><span class="s" style="color: #d14;">'build_ext'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Cython</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Distutils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">build_ext</span></span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="python"><span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="python"><span class="k" style="font-weight: 600;">except</span><span class="idiff left"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">Exception</span></span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Run 2to3 builder if we're on Python 3.x, from</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">@@ -102,16 +101,22 @@ command_classes['build_py'] = build_py</td>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Use epydoc if found</span></span>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="python"><span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pkg_resources</span></span>
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="python"> <span class="n" style="color: #333;">pkg_resources</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">require</span><span class="p">(</span> <span class="s" style="color: #d14;">"epydoc"</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">epydoc.cli</span><span class="p">,</span> <span class="n" style="color: #333;">sys</span><span class="p">,</span> <span class="n" style="color: #333;">os</span><span class="p">,</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span></span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"> <span class="n" style="color: #333;">pkg_resources</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">require</span><span class="p">(</span><span class="s" style="color: #d14;">"epydoc"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">epydoc.cli</span></span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os.path</span></span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Create command class to build API documentation</span></span>
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="python"> <span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">BuildAPIDocs</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">Command</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="python"> <span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">BuildAPIDocs</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">Command</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="python"> <span class="n" style="color: #333;">user_options</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">initialize_options</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="LC112" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">initialize_options</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="LC114" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">finalize_options</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="LC115" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">finalize_options</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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113
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117
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">run</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="LC118" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">run</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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115
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120
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Save working directory and args</span></span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="python"> <span class="n" style="color: #333;">old_argv</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">argv</span></span>
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122
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="python"> <span class="n" style="color: #333;">old_cwd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getcwd</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">@@ -122,18 +127,18 @@ try:</td>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="python"><span class="s" style="color: #d14;"> --docformat=reStructuredText</span></span>
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123
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="python"><span class="s" style="color: #d14;"> --output=../doc/docbuild/html/apidoc"""</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Make output directory</span></span>
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"./doc/docbuild/html/apidoc"</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mkdir</span><span class="p">(</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"./doc/docbuild/html/apidoc"</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left right">"./doc/docbuild/html/apidoc"</span></span><span class="p">):</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mkdir</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left right">"./doc/docbuild/html/apidoc"</span></span><span class="p">)</span></span>
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127
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132
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Move to lib directory (so bx package is in current directory)</span></span>
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128
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chdir</span><span class="p">(</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"./lib"</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chdir</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left right">"./lib"</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Invoke epydoc</span></span>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="python"> <span class="n" style="color: #333;">epydoc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cli</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Restore args and working directory</span></span>
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">argv</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">old_argv</span></span>
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chdir</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">old_cwd</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Add to extra_commands<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chdir</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">old_cwd</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Add to extra_commands</span></span>
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="python"> <span class="n" style="color: #333;">command_classes</span><span class="p">[</span><span class="s" style="color: #d14;">'build_apidocs'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BuildAPIDocs</span></span>
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="python"><span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="python"><span class="k" style="font-weight: 600;">except</span><span class="idiff left"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">Exception</span></span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ---- Extension Modules ----------------------------------------------------</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">@@ -143,81 +148,80 @@ except:</td>
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># _Extension = Extension</span></span>
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Extension = partial(_Extension, extra_compile_args=["-Wno-cpp"])</span></span>
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_extension_modules</span><span class="p">(</span> <span class="n" style="color: #333;">numpy_include</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span> <span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_extension_modules</span><span class="p">(</span><span class="n" style="color: #333;">numpy_include</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="python"> <span class="n" style="color: #333;">extensions</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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154
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Bitsets</span></span>
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="python"> <span class="n" style="color: #333;">extensions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">Extension</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff right"> </span><span class="s" style="color: #d14;">"bx.bitset"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="python"> <span class="idiff left"> </span><span class="p"><span class="idiff">[</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"lib/bx/bitset.pyx"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span></span>
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="python"> <span class="idiff left right"> </span><span class="s" style="color: #d14;">"src/binBits.c"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="python"> <span class="idiff left right"> </span><span class="s" style="color: #d14;">"src/kent/bits.c"</span><span class="p">,</span></span>
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153
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="python"> <span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"src/kent/common.c"</span></span><span class="idiff right"> </span><span class="p">],</span></span>
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154
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="python"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">include_dirs</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="p"><span class="idiff">[</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"src/kent"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"src"</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="python"> <span class="n" style="color: #333;">extensions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">Extension</span></span><span class="p"><span class="idiff right">(</span></span><span class="s" style="color: #d14;">"bx.bitset"</span><span class="p">,</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="python"> <span class="p"><span class="idiff left">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"lib/bx/bitset.pyx"</span></span><span class="p"><span class="idiff right">,</span></span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="python"> <span class="s" style="color: #d14;">"src/binBits.c"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="python"> <span class="s" style="color: #d14;">"src/kent/bits.c"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="python"> <span class="s" style="color: #d14;"><span class="idiff left right">"src/kent/common.c"</span></span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">include_dirs</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"src/kent"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"src"</span></span><span class="p"><span class="idiff right">])</span>)</span></span>
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Interval intersection</span></span>
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156
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="python"> <span class="n" style="color: #333;">extensions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">Extension</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"bx.intervals.intersection"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"lib/bx/intervals/intersection.pyx"</span></span><span class="idiff"> </span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="python"> <span class="n" style="color: #333;">extensions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">Extension</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"bx.intervals.intersection"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"lib/bx/intervals/intersection.pyx"</span></span><span class="p"><span class="idiff right">])</span>)</span></span>
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157
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163
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Alignment object speedups</span></span>
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158
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="python"> <span class="n" style="color: #333;">extensions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">Extension</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"bx.align._core"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"lib/bx/align/_core.pyx"</span></span><span class="idiff"> </span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="python"> <span class="n" style="color: #333;">extensions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">Extension</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"bx.align._core"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"lib/bx/align/_core.pyx"</span></span><span class="p"><span class="idiff right">])</span>)</span></span>
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159
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165
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># NIB reading speedups</span></span>
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="python"> <span class="n" style="color: #333;">extensions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">Extension</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"bx.seq._nib"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"lib/bx/seq/_nib.pyx"</span></span><span class="idiff"> </span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="python"> <span class="n" style="color: #333;">extensions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">Extension</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"bx.seq._nib"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"lib/bx/seq/_nib.pyx"</span></span><span class="p"><span class="idiff right">])</span>)</span></span>
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167
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># 2bit reading speedups</span></span>
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162
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="python"> <span class="n" style="color: #333;">extensions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">Extension</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"bx.seq._twobit"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"lib/bx/seq/_twobit.pyx"</span></span><span class="idiff"> </span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Translation if character / integer strings<span class="idiff left right"> </span></span></span>
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164
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="python"> <span class="n" style="color: #333;">extensions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">Extension</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"bx._seqmapping"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"lib/bx/_seqmapping.pyx"</span></span><span class="idiff"> </span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="python"> <span class="n" style="color: #333;">extensions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">Extension</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"bx.seq._twobit"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"lib/bx/seq/_twobit.pyx"</span></span><span class="p"><span class="idiff right">])</span>)</span></span>
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Translation if character / integer strings</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="python"> <span class="n" style="color: #333;">extensions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">Extension</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"bx._seqmapping"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"lib/bx/_seqmapping.pyx"</span></span><span class="p"><span class="idiff right">])</span>)</span></span>
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165
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># BGZF</span></span>
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="python"> <span class="n" style="color: #333;">extensions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">Extension</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff right"> </span><span class="s" style="color: #d14;">"bx.misc.bgzf"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="python"> <span class="idiff left"> </span><span class="p"><span class="idiff">[</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"lib/bx/misc/bgzf.pyx"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"src/samtools/bgzf.c"</span></span><span class="idiff right"> </span><span class="p">],</span></span>
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168
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="python"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">include_dirs</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="p"><span class="idiff">[</span></span><span class="idiff right"> </span><span class="s" style="color: #d14;">"src/samtools"</span><span class="p">],</span></span>
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169
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="python"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">libraries</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">'z'</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="python"> <span class="n" style="color: #333;">extensions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">Extension</span></span><span class="p"><span class="idiff right">(</span></span><span class="s" style="color: #d14;">"bx.misc.bgzf"</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="python"> <span class="p"><span class="idiff left">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"lib/bx/misc/bgzf.pyx"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"src/samtools/bgzf.c"</span></span><span class="p">],</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">include_dirs</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="p"><span class="idiff right">[</span></span><span class="s" style="color: #d14;">"src/samtools"</span><span class="p">],</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">libraries</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">'z'</span></span><span class="p"><span class="idiff right">])</span>)</span></span>
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="python"> </span>
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># The following extensions won't (currently) compile on windows</span></span>
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">platform</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">system</span><span class="p">()</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span> <span class="s" style="color: #d14;">'Microsoft'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Windows'</span> <span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="python"> </span>
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Interval clustering </span></span>
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="python"> <span class="n" style="color: #333;">extensions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span> <span class="n" style="color: #333;">Extension</span><span class="p">(</span> <span class="s" style="color: #d14;">"bx.intervals.cluster"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="python"> <span class="p">[</span> <span class="s" style="color: #d14;">"lib/bx/intervals/cluster.pyx"</span><span class="p">,</span> </span>
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="python"> <span class="s" style="color: #d14;">"src/cluster.c"</span><span class="p">],</span></span>
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="python"> <span class="n" style="color: #333;">include_dirs</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">"src"</span><span class="p">]</span> <span class="p">)</span> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">platform</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">system</span><span class="p">()</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="s" style="color: #d14;">'Microsoft'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Windows'</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Interval clustering</span></span>
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="python"> <span class="n" style="color: #333;">extensions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">Extension</span><span class="p">(</span><span class="s" style="color: #d14;">"bx.intervals.cluster"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="python"> <span class="p">[</span><span class="s" style="color: #d14;">"lib/bx/intervals/cluster.pyx"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="python"> <span class="s" style="color: #d14;">"src/cluster.c"</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="python"> <span class="n" style="color: #333;">include_dirs</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">"src"</span><span class="p">]))</span></span>
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Position weight matrices</span></span>
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="python"> <span class="n" style="color: #333;">extensions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">Extension</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff right"> </span><span class="s" style="color: #d14;">"bx.pwm._position_weight_matrix"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="python"> <span class="p"><span class="idiff left">[</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"lib/bx/pwm/_position_weight_matrix.pyx"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"src/pwm_utils.c"</span></span><span class="idiff right"> </span><span class="p">],</span></span>
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">include_dirs</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"src"</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="python"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="python"> <span class="n" style="color: #333;">extensions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">Extension</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"bx.motif._pwm"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"lib/bx/motif/_pwm.pyx"</span></span><span class="idiff"> </span><span class="p"><span class="idiff">],</span></span><span class="idiff right"> </span></span>
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="python"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">include_dirs</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">numpy_include</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="python"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="python"> <span class="n" style="color: #333;">extensions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">Extension</span></span><span class="p"><span class="idiff right">(</span></span><span class="s" style="color: #d14;">"bx.pwm._position_weight_matrix"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="python"> <span class="idiff left"> </span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"lib/bx/pwm/_position_weight_matrix.pyx"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"src/pwm_utils.c"</span></span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="python"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">include_dirs</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"src"</span></span><span class="p"><span class="idiff right">])</span>)</span></span>
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="python"> <span class="n" style="color: #333;">extensions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">Extension</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"bx.motif._pwm"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"lib/bx/motif/_pwm.pyx"</span></span><span class="p"><span class="idiff right">],</span></span></span>
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">include_dirs</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">numpy_include</span></span><span class="p"><span class="idiff right">])</span>)</span></span>
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Sparse arrays with summaries organized as trees on disk</span></span>
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<pre style="margin: 0;">-<span id="LC189" class="line" lang="python"> <span class="n" style="color: #333;">extensions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">Extension</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"bx.arrays.array_tree"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"lib/bx/arrays/array_tree.pyx"</span></span><span class="idiff"> </span><span class="p"><span class="idiff">],</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">include_dirs</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">numpy_include</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span></span>
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<pre style="margin: 0;">-<span id="LC190" class="line" lang="python"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="python"> <span class="n" style="color: #333;">extensions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">Extension</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"bx.arrays.array_tree"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"lib/bx/arrays/array_tree.pyx"</span></span><span class="p"><span class="idiff">],</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">include_dirs</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">numpy_include</span></span><span class="p"><span class="idiff right">]))</span></span></span>
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Reading UCSC "big binary index" files</span></span>
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="python"> <span class="n" style="color: #333;">extensions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">Extension</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"bx.bbi.bpt_file"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"lib/bx/bbi/bpt_file.pyx"</span></span><span class="idiff"> </span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="python"> <span class="n" style="color: #333;">extensions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">Extension</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"bx.bbi.cirtree_file"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"lib/bx/bbi/cirtree_file.pyx"</span></span><span class="idiff"> </span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC194" class="line" lang="python"> <span class="n" style="color: #333;">extensions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">Extension</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"bx.bbi.bbi_file"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"lib/bx/bbi/bbi_file.pyx"</span></span><span class="idiff"> </span><span class="p"><span class="idiff">],</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">include_dirs</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">numpy_include</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="python"> <span class="n" style="color: #333;">extensions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">Extension</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"bx.bbi.bigwig_file"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"lib/bx/bbi/bigwig_file.pyx"</span></span><span class="idiff"> </span><span class="p"><span class="idiff">],</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">include_dirs</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">numpy_include</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="python"> <span class="n" style="color: #333;">extensions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">Extension</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"bx.bbi.bigbed_file"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"lib/bx/bbi/bigbed_file.pyx"</span></span><span class="idiff"> </span><span class="p"><span class="idiff">],</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">include_dirs</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">numpy_include</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="python"> <span class="n" style="color: #333;">extensions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">Extension</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"bx.bbi.bpt_file"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"lib/bx/bbi/bpt_file.pyx"</span></span><span class="p"><span class="idiff right">])</span>)</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="python"> <span class="n" style="color: #333;">extensions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">Extension</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"bx.bbi.cirtree_file"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"lib/bx/bbi/cirtree_file.pyx"</span></span><span class="p"><span class="idiff right">])</span>)</span></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="python"> <span class="n" style="color: #333;">extensions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">Extension</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"bx.bbi.bbi_file"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"lib/bx/bbi/bbi_file.pyx"</span></span><span class="p"><span class="idiff">],</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">include_dirs</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">numpy_include</span></span><span class="p"><span class="idiff right">])</span>)</span></span>
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="python"> <span class="n" style="color: #333;">extensions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">Extension</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"bx.bbi.bigwig_file"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"lib/bx/bbi/bigwig_file.pyx"</span></span><span class="p"><span class="idiff">],</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">include_dirs</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">numpy_include</span></span><span class="p"><span class="idiff right">])</span>)</span></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="python"> <span class="n" style="color: #333;">extensions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">Extension</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"bx.bbi.bigbed_file"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"lib/bx/bbi/bigbed_file.pyx"</span></span><span class="p"><span class="idiff">],</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">include_dirs</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">numpy_include</span></span><span class="p"><span class="idiff right">])</span>)</span></span>
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201
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="python"></span>
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198
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202
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># EPO and Chain arithmetics and IO speedups</span></span>
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199
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="python"> <span class="n" style="color: #333;">extensions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">Extension</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"bx.align._epo"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"lib/bx/align/_epo.pyx"</span></span><span class="idiff"> </span><span class="p"><span class="idiff">],</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">include_dirs</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">numpy_include</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="python"> <span class="n" style="color: #333;">extensions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">Extension</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"bx.align._epo"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"lib/bx/align/_epo.pyx"</span></span><span class="p"><span class="idiff">],</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">include_dirs</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">numpy_include</span></span><span class="p"><span class="idiff right">])</span>)</span></span>
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200
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="python"></span>
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201
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205
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Reading UCSC bed and wiggle formats</span></span>
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202
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="python"> <span class="n" style="color: #333;">extensions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span> <span class="n" style="color: #333;">Extension</span><span class="p">(</span> <span class="s" style="color: #d14;">"bx.arrays.bed"</span><span class="p">,</span> <span class="p">[</span> <span class="s" style="color: #d14;">"lib/bx/arrays/bed.pyx"</span> <span class="p">]</span> <span class="p">)</span> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="python"> <span class="n" style="color: #333;">extensions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">Extension</span><span class="p">(</span><span class="s" style="color: #d14;">"bx.arrays.bed"</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">"lib/bx/arrays/bed.pyx"</span><span class="p">]))</span></span>
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<pre style="margin: 0;"> <span id="LC208" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># CpG masking</span></span>
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="python"> <span class="n" style="color: #333;">extensions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">Extension</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"bx.align.sitemask._cpg"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> \</span></span>
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="python"> <span class="idiff left"> </span><span class="p"><span class="idiff">[</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"lib/bx/align/sitemask/_cpg.pyx"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span></span>
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<pre style="margin: 0;">-<span id="LC209" class="line" lang="python"> <span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"lib/bx/align/sitemask/find_cpg.c"</span></span><span class="idiff"> </span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC210" class="line" lang="python"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="python"> <span class="n" style="color: #333;">extensions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">Extension</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"bx.align.sitemask._cpg"</span></span><span class="p"><span class="idiff right">,</span></span></span>
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="python"> <span class="p"><span class="idiff left">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"lib/bx/align/sitemask/_cpg.pyx"</span></span><span class="p"><span class="idiff right">,</span></span></span>
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="python"> <span class="s" style="color: #d14;"><span class="idiff left">"lib/bx/align/sitemask/find_cpg.c"</span></span><span class="p"><span class="idiff right">])</span>)</span></span>
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Counting n-grams in integer strings</span></span>
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<pre style="margin: 0;">-<span id="LC212" class="line" lang="python"> <span class="n" style="color: #333;">extensions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">Extension</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"bx.intseq.ngramcount"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"lib/bx/intseq/ngramcount.pyx"</span></span><span class="idiff right"> </span><span class="p">],</span></span>
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<pre style="margin: 0;">-<span id="LC213" class="line" lang="python"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">include_dirs</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"src"</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="python"> <span class="n" style="color: #333;">extensions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">Extension</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"bx.intseq.ngramcount"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff right">"lib/bx/intseq/ngramcount.pyx"</span></span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">include_dirs</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"src"</span></span><span class="p"><span class="idiff right">])</span>)</span></span>
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Seekable access to bzip2 files</span></span>
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="python"> <span class="n" style="color: #333;">extensions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span> <span class="n" style="color: #333;">Extension</span><span class="p">(</span> <span class="s" style="color: #d14;">"bx.misc._seekbzip2"</span><span class="p">,</span> </span>
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<pre style="margin: 0;">-<span id="LC217" class="line" lang="python"> <span class="p">[</span> <span class="s" style="color: #d14;">"lib/bx/misc/_seekbzip2.pyx"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC218" class="line" lang="python"> <span class="s" style="color: #d14;">"src/bunzip/micro-bunzip.c"</span> <span class="p">],</span></span>
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<pre style="margin: 0;">-<span id="LC219" class="line" lang="python"> <span class="n" style="color: #333;">include_dirs</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span> <span class="s" style="color: #d14;">"src/bunzip"</span> <span class="p">]</span> <span class="p">)</span> <span class="p">)</span> </span>
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<pre style="margin: 0;">-<span id="LC220" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">extensions</span> </span>
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<pre style="margin: 0;">-<span id="LC221" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="python"> <span class="n" style="color: #333;">extensions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">Extension</span><span class="p">(</span><span class="s" style="color: #d14;">"bx.misc._seekbzip2"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="python"> <span class="p">[</span><span class="s" style="color: #d14;">"lib/bx/misc/_seekbzip2.pyx"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="python"> <span class="s" style="color: #d14;">"src/bunzip/micro-bunzip.c"</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="python"> <span class="n" style="color: #333;">include_dirs</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">"src/bunzip"</span><span class="p">]))</span></span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">extensions</span></span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">__name__</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"__main__"</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="python"> <span class="n" style="color: #333;">main</span><span class="p">()</span></span></pre>
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