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Étienne Mollier pushed to branch upstream at <a href="https://salsa.debian.org/med-team/python-dnaio">Debian Med / python-dnaio</a>
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Commits:
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<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/python-dnaio/-/commit/40879644044aca1c849a2d9722d5d3acaa3d0f87">40879644</a></strong>
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<span> by Étienne Mollier </span> <i> at 2024-10-09T20:49:49+02:00 </i>
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<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>New upstream version 1.2.2</pre>
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5 changed files:
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CHANGES.rst
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src/dnaio/_core.pyx
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<a href="#a4b247ff1a44413cf691bb93ac7d67db5ee22cea">
src/dnaio/bam.h
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+
tests/data/missing_quals.bam
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tests/test_internal.py
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Changes:
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<li id="4990be809a537bf86e4be2fe2e8251c83d8bd129">
<a href="https://salsa.debian.org/med-team/python-dnaio/-/commit/40879644044aca1c849a2d9722d5d3acaa3d0f87#4990be809a537bf86e4be2fe2e8251c83d8bd129"><strong style="font-weight: 600;">CHANGES.rst</strong></a>
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<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -2,6 +2,11 @@</td>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2" class="line" lang="plaintext">Changelog</span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3" class="line" lang="plaintext">=========</span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC5" class="line" lang="plaintext">v1.2.2 (2024-10-04)</span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC6" class="line" lang="plaintext">-------------------</span>
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<td class="new_line diff-line-num new" data-linenumber="7" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC7" class="line" lang="plaintext">* :pr:`139`: Fix an error that occurred when decoding BAM records with missing</span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC8" class="line" lang="plaintext"> quality values. These are now converted to ``None``.</span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC9" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC10" class="line" lang="plaintext">v1.2.1 (2024-06-17)</span>
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<li id="72ff21bf4040f97f9c5919d676e807b4117d01b7">
<a href="https://salsa.debian.org/med-team/python-dnaio/-/commit/40879644044aca1c849a2d9722d5d3acaa3d0f87#72ff21bf4040f97f9c5919d676e807b4117d01b7"><strong style="font-weight: 600;">src/dnaio/_core.pyx</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="824" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="824" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -824,10 +824,14 @@ cdef class BamIter:</td>
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<td class="new_line diff-line-num" data-linenumber="824" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC824" class="line" lang="cython"> <span class="n" style="color: #333333;">bam_qual_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">bam_seq_start</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333333;">encoded_seq_length</span></span>
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<td class="old_line diff-line-num" data-linenumber="825" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
825
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825
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC825" class="line" lang="cython"> <span class="n" style="color: #333333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #990000; font-weight: 600;">PyUnicode_New</span><span class="p">(</span><span class="n" style="color: #333333;">name_length</span><span class="p">,</span> <span class="mi" style="color: #009999;">127</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="826" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
826
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<td class="new_line diff-line-num" data-linenumber="826" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
826
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC826" class="line" lang="cython"> <span class="n" style="color: #333333;">sequence</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #990000; font-weight: 600;">PyUnicode_New</span><span class="p">(</span><span class="n" style="color: #333333;">seq_length</span><span class="p">,</span> <span class="mi" style="color: #009999;">127</span><span class="p">)</span></span>
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827
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<td class="new_line diff-line-num old" data-linenumber="827" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC827" class="line" lang="cython"> <span class="n" style="color: #333333;">qualities</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #990000; font-weight: 600;">PyUnicode_New</span><span class="p">(</span><span class="n" style="color: #333333;">seq_length</span><span class="p">,</span> <span class="mi" style="color: #009999;">127</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="828" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
828
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<td class="new_line diff-line-num" data-linenumber="827" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
827
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC827" class="line" lang="cython"> <span class="nf" style="color: #990000; font-weight: 600;">memcpy</span><span class="p">(</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333333;">uint8_t</span> <span class="o" style="font-weight: 600;">*></span><span class="nf" style="color: #990000; font-weight: 600;">PyUnicode_DATA</span><span class="p">(</span><span class="n" style="color: #333333;">name</span><span class="p">),</span> <span class="n" style="color: #333333;">bam_name_start</span><span class="p">,</span> <span class="n" style="color: #333333;">name_length</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="829" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
829
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<td class="new_line diff-line-num" data-linenumber="828" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
828
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC828" class="line" lang="cython"> <span class="nf" style="color: #990000; font-weight: 600;">decode_bam_sequence</span><span class="p">(</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333333;">uint8_t</span> <span class="o" style="font-weight: 600;">*></span><span class="nf" style="color: #990000; font-weight: 600;">PyUnicode_DATA</span><span class="p">(</span><span class="n" style="color: #333333;">sequence</span><span class="p">),</span> <span class="n" style="color: #333333;">bam_seq_start</span><span class="p">,</span> <span class="n" style="color: #333333;">seq_length</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="830" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
830
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<td class="new_line diff-line-num old" data-linenumber="829" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC830" class="line" lang="cython"> <span class="nf" style="color: #990000; font-weight: 600;">decode_bam_qualities</span><span class="p">(</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333333;">uint8_t</span> <span class="o" style="font-weight: 600;">*></span><span class="nf" style="color: #990000; font-weight: 600;">PyUnicode_DATA</span><span class="p">(</span><span class="n" style="color: #333333;">qualities</span><span class="p">),</span> <span class="n" style="color: #333333;">bam_qual_start</span><span class="p">,</span> <span class="n" style="color: #333333;">seq_length</span><span class="p">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="831" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="829" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
829
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC829" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">seq_length</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333333;">bam_qual_start</span><span class="p">[</span><span class="mi" style="color: #009999;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mh" style="color: #009999;">0xff</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="831" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="830" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
830
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC830" class="line" lang="cython"> <span class="c1" style="color: #999988; font-style: italic;"># 0xff means qualities are missing.</span></span>
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<td class="old_line diff-line-num new" data-linenumber="831" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="831" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
831
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC831" class="line" lang="cython"> <span class="n" style="color: #333333;">qualities</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999999;">None</span></span>
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<td class="old_line diff-line-num new" data-linenumber="831" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="832" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
832
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC832" class="line" lang="cython"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="831" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="833" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
833
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC833" class="line" lang="cython"> <span class="n" style="color: #333333;">qualities</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #990000; font-weight: 600;">PyUnicode_New</span><span class="p">(</span><span class="n" style="color: #333333;">seq_length</span><span class="p">,</span> <span class="mi" style="color: #009999;">127</span><span class="p">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="831" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="834" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
834
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC834" class="line" lang="cython"> <span class="nf" style="color: #990000; font-weight: 600;">decode_bam_qualities</span><span class="p">(</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333333;">uint8_t</span> <span class="o" style="font-weight: 600;">*></span><span class="nf" style="color: #990000; font-weight: 600;">PyUnicode_DATA</span><span class="p">(</span><span class="n" style="color: #333333;">qualities</span><span class="p">),</span> <span class="n" style="color: #333333;">bam_qual_start</span><span class="p">,</span> <span class="n" style="color: #333333;">seq_length</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="831" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
831
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<td class="new_line diff-line-num" data-linenumber="835" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
835
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC835" class="line" lang="cython"> <span class="n" style="color: #333333;">seq_record</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">SequenceRecord</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">__new__</span><span class="p">(</span><span class="n" style="color: #333333;">SequenceRecord</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="832" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
832
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<td class="new_line diff-line-num" data-linenumber="836" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
836
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC836" class="line" lang="cython"> <span class="n" style="color: #333333;">seq_record</span><span class="p">.</span><span class="n" style="color: #333333;">_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">name</span></span>
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<td class="old_line diff-line-num" data-linenumber="833" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
833
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<td class="new_line diff-line-num" data-linenumber="837" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
837
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC837" class="line" lang="cython"> <span class="n" style="color: #333333;">seq_record</span><span class="p">.</span><span class="n" style="color: #333333;">_sequence</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">sequence</span></span>
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<li id="a4b247ff1a44413cf691bb93ac7d67db5ee22cea">
<a href="https://salsa.debian.org/med-team/python-dnaio/-/commit/40879644044aca1c849a2d9722d5d3acaa3d0f87#a4b247ff1a44413cf691bb93ac7d67db5ee22cea"><strong style="font-weight: 600;">src/dnaio/bam.h</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="13" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="13" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -13,6 +13,7 @@</td>
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<td class="old_line diff-line-num" data-linenumber="13" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
13
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<td class="new_line diff-line-num" data-linenumber="13" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
13
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC13" class="line" lang="c"><span class="cp" style="color: #999999; font-weight: 600;">#endif</span></span>
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<td class="old_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
14
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<td class="new_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
14
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC14" class="line" lang="c"></span>
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<td class="old_line diff-line-num" data-linenumber="15" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
15
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<td class="new_line diff-line-num" data-linenumber="15" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
15
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC15" class="line" lang="c"><span class="cp" style="color: #999999; font-weight: 600;">#define COMPILER_HAS_TARGET (GCC_AT_LEAST(4, 8) || CLANG_COMPILER_HAS(__target__))</span></span>
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16
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC16" class="line" lang="c"><span class="cp" style="color: #999999; font-weight: 600;">#define COMPILER_HAS_CONSTRUCTOR (__GNUC__ || CLANG_COMPILER_HAS(constructor))</span></span>
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17
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC17" class="line" lang="c"><span class="cp" style="color: #999999; font-weight: 600;">#define COMPILER_HAS_OPTIMIZE (GCC_AT_LEAST(4,4) || CLANG_COMPILER_HAS(optimize))</span></span>
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18
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC18" class="line" lang="c"></span>
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19
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC19" class="line" lang="c"><span class="cp" style="color: #999999; font-weight: 600;">#if defined(__x86_64__) || defined(_M_X64)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="56" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
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<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -56,7 +57,11 @@ decode_bam_sequence_default(uint8_t *dest, const uint8_t *encoded_sequence, size</td>
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56
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57
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC57" class="line" lang="c"> <span class="p">}</span></span>
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58
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC58" class="line" lang="c"><span class="p">}</span></span>
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59
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC59" class="line" lang="c"></span>
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<td class="old_line diff-line-num old" data-linenumber="59" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
59
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<td class="new_line diff-line-num old" data-linenumber="60" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC59" class="line" lang="c"><span class="cp" style="color: #999999; font-weight: 600;">#if COMPILER_HAS_TARGET && BUILD_IS_X86_64</span></span>
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<td class="old_line diff-line-num new" data-linenumber="60" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="60" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
60
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC60" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #445588; font-weight: 600;">void</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333333;">decode_bam_sequence</span><span class="p">)(</span></span>
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<td class="new_line diff-line-num new" data-linenumber="61" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
61
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC61" class="line" lang="c"> <span class="kt" style="color: #445588; font-weight: 600;">uint8_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333333;">dest</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #445588; font-weight: 600;">uint8_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333333;">encoded_sequence</span><span class="p">,</span> <span class="kt" style="color: #445588; font-weight: 600;">size_t</span> <span class="n" style="color: #333333;">length</span></span>
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<td class="new_line diff-line-num new" data-linenumber="62" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
62
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC62" class="line" lang="c"><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">decode_bam_sequence_default</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="63" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
63
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC63" class="line" lang="c"></span>
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<td class="new_line diff-line-num new" data-linenumber="64" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
64
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC64" class="line" lang="c"><span class="cp" style="color: #999999; font-weight: 600;">#if COMPILER_HAS_TARGET && COMPILER_HAS_CONSTRUCTOR && BUILD_IS_X86_64</span></span>
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<td class="old_line diff-line-num" data-linenumber="60" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
60
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<td class="new_line diff-line-num" data-linenumber="65" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
65
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC65" class="line" lang="c"><span class="n" style="color: #333333;">__attribute__</span><span class="p">((</span><span class="n" style="color: #333333;">__target__</span><span class="p">(</span><span class="s" style="color: #dd1144;">"ssse3"</span><span class="p">)))</span></span>
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<td class="old_line diff-line-num" data-linenumber="61" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
61
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<td class="new_line diff-line-num" data-linenumber="66" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
66
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC66" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #445588; font-weight: 600;">void</span> </span>
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<td class="old_line diff-line-num" data-linenumber="62" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
62
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<td class="new_line diff-line-num" data-linenumber="67" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
67
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC67" class="line" lang="c"><span class="nf" style="color: #990000; font-weight: 600;">decode_bam_sequence_ssse3</span><span class="p">(</span><span class="kt" style="color: #445588; font-weight: 600;">uint8_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333333;">dest</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #445588; font-weight: 600;">uint8_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333333;">encoded_sequence</span><span class="p">,</span> <span class="kt" style="color: #445588; font-weight: 600;">size_t</span> <span class="n" style="color: #333333;">length</span><span class="p">)</span> </span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="71" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -66,79 +71,41 @@ decode_bam_sequence_ssse3(uint8_t *dest, const uint8_t *encoded_sequence, size_t</td>
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66
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71
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC71" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #445588; font-weight: 600;">uint8_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333333;">dest_end_ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">dest</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333333;">length</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="67" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
67
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<td class="new_line diff-line-num" data-linenumber="72" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
72
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC72" class="line" lang="c"> <span class="kt" style="color: #445588; font-weight: 600;">uint8_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333333;">dest_cursor</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">dest</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="68" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
68
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<td class="new_line diff-line-num" data-linenumber="73" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
73
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC73" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #445588; font-weight: 600;">uint8_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333333;">encoded_cursor</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">encoded_sequence</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="69" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
69
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<td class="new_line diff-line-num old" data-linenumber="74" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC69" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #445588; font-weight: 600;">uint8_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333333;">dest_vec_end_ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">dest_end_ptr</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">(</span><span class="mi" style="color: #009999;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333333;">__m128i</span><span class="p">));</span></span>
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<td class="old_line diff-line-num old" data-linenumber="70" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
70
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<td class="new_line diff-line-num old" data-linenumber="74" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC70" class="line" lang="c"> <span class="n" style="color: #333333;">__m128i</span> <span class="n" style="color: #333333;">first_upper_shuffle</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">_mm_setr_epi8</span><span class="p">(</span></span>
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<td class="old_line diff-line-num old" data-linenumber="71" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
71
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<td class="new_line diff-line-num old" data-linenumber="74" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC71" class="line" lang="c"> <span class="mi" style="color: #009999;">0</span><span class="p">,</span> <span class="mh" style="color: #009999;">0xff</span><span class="p">,</span> <span class="mi" style="color: #009999;">1</span><span class="p">,</span> <span class="mh" style="color: #009999;">0xff</span><span class="p">,</span> <span class="mi" style="color: #009999;">2</span><span class="p">,</span> <span class="mh" style="color: #009999;">0xff</span><span class="p">,</span> <span class="mi" style="color: #009999;">3</span><span class="p">,</span> <span class="mh" style="color: #009999;">0xff</span><span class="p">,</span> <span class="mi" style="color: #009999;">4</span><span class="p">,</span> <span class="mh" style="color: #009999;">0xff</span><span class="p">,</span> <span class="mi" style="color: #009999;">5</span><span class="p">,</span> <span class="mh" style="color: #009999;">0xff</span><span class="p">,</span> <span class="mi" style="color: #009999;">6</span><span class="p">,</span> <span class="mh" style="color: #009999;">0xff</span><span class="p">,</span> <span class="mi" style="color: #009999;">7</span><span class="p">,</span> <span class="mh" style="color: #009999;">0xff</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="72" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
72
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<td class="new_line diff-line-num old" data-linenumber="74" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC72" class="line" lang="c"> <span class="n" style="color: #333333;">__m128i</span> <span class="n" style="color: #333333;">first_lower_shuffle</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">_mm_setr_epi8</span><span class="p">(</span></span>
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<td class="old_line diff-line-num old" data-linenumber="73" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
73
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<td class="new_line diff-line-num old" data-linenumber="74" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC73" class="line" lang="c"> <span class="mh" style="color: #009999;">0xff</span><span class="p">,</span> <span class="mi" style="color: #009999;">0</span><span class="p">,</span> <span class="mh" style="color: #009999;">0xff</span><span class="p">,</span> <span class="mi" style="color: #009999;">1</span><span class="p">,</span> <span class="mh" style="color: #009999;">0xff</span><span class="p">,</span> <span class="mi" style="color: #009999;">2</span><span class="p">,</span> <span class="mh" style="color: #009999;">0xff</span><span class="p">,</span> <span class="mi" style="color: #009999;">3</span><span class="p">,</span> <span class="mh" style="color: #009999;">0xff</span><span class="p">,</span> <span class="mi" style="color: #009999;">4</span><span class="p">,</span> <span class="mh" style="color: #009999;">0xff</span><span class="p">,</span> <span class="mi" style="color: #009999;">5</span><span class="p">,</span> <span class="mh" style="color: #009999;">0xff</span><span class="p">,</span> <span class="mi" style="color: #009999;">6</span><span class="p">,</span> <span class="mh" style="color: #009999;">0xff</span><span class="p">,</span> <span class="mi" style="color: #009999;">7</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="74" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
74
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<td class="new_line diff-line-num old" data-linenumber="74" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC74" class="line" lang="c"> <span class="n" style="color: #333333;">__m128i</span> <span class="n" style="color: #333333;">second_upper_shuffle</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">_mm_setr_epi8</span><span class="p">(</span></span>
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<td class="old_line diff-line-num old" data-linenumber="75" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
75
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<td class="new_line diff-line-num old" data-linenumber="74" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC75" class="line" lang="c"> <span class="mi" style="color: #009999;">8</span><span class="p">,</span> <span class="mh" style="color: #009999;">0xff</span><span class="p">,</span> <span class="mi" style="color: #009999;">9</span><span class="p">,</span> <span class="mh" style="color: #009999;">0xff</span><span class="p">,</span> <span class="mi" style="color: #009999;">10</span><span class="p">,</span> <span class="mh" style="color: #009999;">0xff</span><span class="p">,</span> <span class="mi" style="color: #009999;">11</span><span class="p">,</span> <span class="mh" style="color: #009999;">0xff</span><span class="p">,</span> <span class="mi" style="color: #009999;">12</span><span class="p">,</span> <span class="mh" style="color: #009999;">0xff</span><span class="p">,</span> <span class="mi" style="color: #009999;">13</span><span class="p">,</span> <span class="mh" style="color: #009999;">0xff</span><span class="p">,</span> <span class="mi" style="color: #009999;">14</span><span class="p">,</span> <span class="mh" style="color: #009999;">0xff</span><span class="p">,</span> <span class="mi" style="color: #009999;">15</span><span class="p">,</span> <span class="mh" style="color: #009999;">0xff</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="76" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
76
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<td class="new_line diff-line-num old" data-linenumber="74" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC76" class="line" lang="c"> <span class="n" style="color: #333333;">__m128i</span> <span class="n" style="color: #333333;">second_lower_shuffle</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">_mm_setr_epi8</span><span class="p">(</span></span>
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<td class="old_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
77
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<td class="new_line diff-line-num old" data-linenumber="74" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC77" class="line" lang="c"> <span class="mh" style="color: #009999;">0xff</span><span class="p">,</span> <span class="mi" style="color: #009999;">8</span><span class="p">,</span> <span class="mh" style="color: #009999;">0xff</span><span class="p">,</span> <span class="mi" style="color: #009999;">9</span><span class="p">,</span> <span class="mh" style="color: #009999;">0xff</span><span class="p">,</span> <span class="mi" style="color: #009999;">10</span><span class="p">,</span> <span class="mh" style="color: #009999;">0xff</span><span class="p">,</span> <span class="mi" style="color: #009999;">11</span><span class="p">,</span> <span class="mh" style="color: #009999;">0xff</span><span class="p">,</span> <span class="mi" style="color: #009999;">12</span><span class="p">,</span> <span class="mh" style="color: #009999;">0xff</span><span class="p">,</span> <span class="mi" style="color: #009999;">13</span><span class="p">,</span> <span class="mh" style="color: #009999;">0xff</span><span class="p">,</span> <span class="mi" style="color: #009999;">14</span><span class="p">,</span> <span class="mh" style="color: #009999;">0xff</span><span class="p">,</span> <span class="mi" style="color: #009999;">15</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="78" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="74" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
74
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC74" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #445588; font-weight: 600;">uint8_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333333;">dest_vec_end_ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">dest_end_ptr</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">(</span><span class="mi" style="color: #009999;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333333;">__m128i</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #009999;">1</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="78" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
78
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<td class="new_line diff-line-num" data-linenumber="75" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
75
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC75" class="line" lang="c"> <span class="n" style="color: #333333;">__m128i</span> <span class="n" style="color: #333333;">nuc_lookup_vec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">_mm_lddqu_si128</span><span class="p">((</span><span class="n" style="color: #333333;">__m128i</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333333;">nuc_lookup</span><span class="p">);</span></span>
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79
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<td class="new_line diff-line-num old" data-linenumber="76" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC79" class="line" lang="c"> <span class="cm" style="color: #999988; font-style: italic;">/* Work on 16 encoded characters at the time resulting in 32 decoded characters</span></span>
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80
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<td class="new_line diff-line-num old" data-linenumber="76" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC80" class="line" lang="c"><span class="cm" style="color: #999988; font-style: italic;"> Examples are given for 8 encoded characters A until H to keep it readable.</span></span>
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<td class="old_line diff-line-num old" data-linenumber="81" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
81
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<td class="new_line diff-line-num old" data-linenumber="76" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC81" class="line" lang="c"><span class="cm" style="color: #999988; font-style: italic;"> Encoded stored as |AB|CD|EF|GH|</span></span>
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<td class="old_line diff-line-num old" data-linenumber="82" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
82
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<td class="new_line diff-line-num old" data-linenumber="76" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC82" class="line" lang="c"><span class="cm" style="color: #999988; font-style: italic;"> Shuffle into |AB|00|CD|00|EF|00|GH|00| and</span></span>
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<td class="old_line diff-line-num old" data-linenumber="83" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
83
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<td class="new_line diff-line-num old" data-linenumber="76" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC83" class="line" lang="c"><span class="cm" style="color: #999988; font-style: italic;"> |00|AB|00|CD|00|EF|00|GH|</span></span>
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<td class="old_line diff-line-num old" data-linenumber="84" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
84
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<td class="new_line diff-line-num old" data-linenumber="76" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC84" class="line" lang="c"><span class="cm" style="color: #999988; font-style: italic;"> Shift upper to the right resulting into</span></span>
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<td class="old_line diff-line-num old" data-linenumber="85" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
85
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<td class="new_line diff-line-num old" data-linenumber="76" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC85" class="line" lang="c"><span class="cm" style="color: #999988; font-style: italic;"> |0A|B0|0C|D0|0E|F0|0G|H0| and</span></span>
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<td class="old_line diff-line-num old" data-linenumber="86" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
86
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<td class="new_line diff-line-num old" data-linenumber="76" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC86" class="line" lang="c"><span class="cm" style="color: #999988; font-style: italic;"> |00|AB|00|CD|00|EF|00|GH|</span></span>
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<td class="old_line diff-line-num old" data-linenumber="87" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
87
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<td class="new_line diff-line-num old" data-linenumber="76" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC87" class="line" lang="c"><span class="cm" style="color: #999988; font-style: italic;"> Merge with or resulting into (X stands for garbage)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="88" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
88
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<td class="new_line diff-line-num old" data-linenumber="76" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC88" class="line" lang="c"><span class="cm" style="color: #999988; font-style: italic;"> |0A|XB|0C|XD|0E|XF|0G|XH|</span></span>
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<td class="old_line diff-line-num old" data-linenumber="89" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
89
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<td class="new_line diff-line-num old" data-linenumber="76" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC89" class="line" lang="c"><span class="cm" style="color: #999988; font-style: italic;"> Bitwise and with 0b1111 leads to:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="90" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
90
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<td class="new_line diff-line-num old" data-linenumber="76" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC90" class="line" lang="c"><span class="cm" style="color: #999988; font-style: italic;"> |0A|0B|0C|0D|0E|0F|0G|0H|</span></span>
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<td class="old_line diff-line-num old" data-linenumber="91" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
91
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<td class="new_line diff-line-num old" data-linenumber="76" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC91" class="line" lang="c"><span class="cm" style="color: #999988; font-style: italic;"> We can use the resulting 4-bit integers as indexes for the shuffle of</span></span>
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<td class="old_line diff-line-num old" data-linenumber="92" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
92
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<td class="new_line diff-line-num old" data-linenumber="76" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC92" class="line" lang="c"><span class="cm" style="color: #999988; font-style: italic;"> the nucleotide lookup. */</span></span>
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<td class="old_line diff-line-num new" data-linenumber="93" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="76" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
76
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC76" class="line" lang="c"> <span class="cm" style="color: #999988; font-style: italic;">/* Nucleotides are encoded 4-bits per nucleotide and stored in 8-bit bytes</span></span>
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<td class="old_line diff-line-num new" data-linenumber="93" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="77" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
77
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC77" class="line" lang="c"><span class="cm" style="color: #999988; font-style: italic;"> as follows: |AB|CD|EF|GH|. The 4-bit codes (going from 0-15) can be used</span></span>
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<td class="old_line diff-line-num new" data-linenumber="93" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="78" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
78
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC78" class="line" lang="c"><span class="cm" style="color: #999988; font-style: italic;"> together with the pshufb instruction as a lookup table. The most efficient</span></span>
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<td class="old_line diff-line-num new" data-linenumber="93" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="79" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
79
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC79" class="line" lang="c"><span class="cm" style="color: #999988; font-style: italic;"> the upper codes (|A|C|E|G|) and one with the lower codes (|B|D|F|H|).</span></span>
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<td class="new_line diff-line-num new" data-linenumber="80" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
80
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC80" class="line" lang="c"><span class="cm" style="color: #999988; font-style: italic;"> The lookup can then be performed and the resulting vectors can be</span></span>
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<td class="old_line diff-line-num new" data-linenumber="93" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="81" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
81
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC81" class="line" lang="c"><span class="cm" style="color: #999988; font-style: italic;"> interleaved again using the unpack instructions. */</span></span>
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<td class="old_line diff-line-num" data-linenumber="93" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
93
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<td class="new_line diff-line-num" data-linenumber="82" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
82
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC82" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333333;">dest_cursor</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333333;">dest_vec_end_ptr</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="94" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
94
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<td class="new_line diff-line-num" data-linenumber="83" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
83
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC83" class="line" lang="c"> <span class="n" style="color: #333333;">__m128i</span> <span class="n" style="color: #333333;">encoded</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">_mm_lddqu_si128</span><span class="p">((</span><span class="n" style="color: #333333;">__m128i</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333333;">encoded_cursor</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="95" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
95
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<td class="new_line diff-line-num old" data-linenumber="84" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC95" class="line" lang="c"></span>
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<td class="old_line diff-line-num old" data-linenumber="96" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
96
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<td class="new_line diff-line-num old" data-linenumber="84" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC96" class="line" lang="c"> <span class="n" style="color: #333333;"><span class="idiff left deletion" style="background-color: #fac5cd;">__m128i</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333333;"><span class="idiff deletion" style="background-color: #fac5cd;">first_upper</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">=</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333333;"><span class="idiff deletion" style="background-color: #fac5cd;">_mm_shuffle_epi8</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">(</span></span><span class="n" style="color: #333333;"><span class="idiff deletion" style="background-color: #fac5cd;">encoded</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333333;"><span class="idiff right deletion" style="background-color: #fac5cd;">first_upper_shuffle</span></span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="97" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
97
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<td class="new_line diff-line-num old" data-linenumber="84" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC97" class="line" lang="c"> <span class="n" style="color: #333333;">__m128i</span> <span class="n" style="color: #333333;"><span class="idiff left deletion" style="background-color: #fac5cd;">first</span>_lower</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">_mm_<span class="idiff deletion" style="background-color: #fac5cd;">shuffle_epi8</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">(</span></span><span class="n" style="color: #333333;"><span class="idiff deletion" style="background-color: #fac5cd;">encoded</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333333;"><span class="idiff right deletion" style="background-color: #fac5cd;">first_lower_shuffle</span></span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="98" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
98
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<td class="new_line diff-line-num old" data-linenumber="84" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC98" class="line" lang="c"> <span class="n" style="color: #333333;">__m128i</span> <span class="n" style="color: #333333;"><span class="idiff left deletion" style="background-color: #fac5cd;">shifted_first</span>_upper</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">_mm_s<span class="idiff deletion" style="background-color: #fac5cd;">rli_epi64</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">(</span></span><span class="n" style="color: #333333;"><span class="idiff deletion" style="background-color: #fac5cd;">first_upper</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="mi" style="color: #009999;"><span class="idiff right deletion" style="background-color: #fac5cd;">4</span></span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="99" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
99
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<td class="new_line diff-line-num old" data-linenumber="84" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC99" class="line" lang="c"> <span class="n" style="color: #333333;">__m128i</span> <span class="n" style="color: #333333;"><span class="idiff left deletion" style="background-color: #fac5cd;">first_merged</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">=</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333333;"><span class="idiff deletion" style="background-color: #fac5cd;">_mm_or_si128</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">(</span></span><span class="n" style="color: #333333;"><span class="idiff deletion" style="background-color: #fac5cd;">shifted_first_upper</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333333;"><span class="idiff right deletion" style="background-color: #fac5cd;">first</span>_lower</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="100" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
100
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<td class="new_line diff-line-num old" data-linenumber="84" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC100" class="line" lang="c"> <span class="n" style="color: #333333;">__m128i</span> <span class="n" style="color: #333333;">first_<span class="idiff left deletion" style="background-color: #fac5cd;">indexes</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">=</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333333;"><span class="idiff deletion" style="background-color: #fac5cd;">_mm_and_si128</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">(</span></span><span class="n" style="color: #333333;"><span class="idiff deletion" style="background-color: #fac5cd;">first_merged</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333333;"><span class="idiff deletion" style="background-color: #fac5cd;">_mm_set1_epi8</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">(</span></span><span class="mi" style="color: #009999;"><span class="idiff deletion" style="background-color: #fac5cd;">0</span></span><span class="n" style="color: #333333;"><span class="idiff deletion" style="background-color: #fac5cd;">b1111</span></span><span class="p"><span class="idiff right deletion" style="background-color: #fac5cd;">)</span>);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="101" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
101
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<td class="new_line diff-line-num old" data-linenumber="84" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC101" class="line" lang="c"> <span class="n" style="color: #333333;">__m128i</span> <span class="n" style="color: #333333;"><span class="idiff left deletion" style="background-color: #fac5cd;">first</span>_nucleotides</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">_mm_<span class="idiff deletion" style="background-color: #fac5cd;">shuffle</span>_epi8</span><span class="p">(</span><span class="n" style="color: #333333;">nuc<span class="idiff deletion" style="background-color: #fac5cd;">_lookup_vec</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333333;"><span class="idiff right deletion" style="background-color: #fac5cd;">first_indexes</span></span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="102" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="84" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
84
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC84" class="line" lang="c"> <span class="n" style="color: #333333;">__m128i</span> <span class="n" style="color: #333333;">encoded_upper</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">_mm_srli_epi64</span><span class="p">(</span><span class="n" style="color: #333333;">encoded</span><span class="p">,</span> <span class="mi" style="color: #009999;">4</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="102" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="85" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
85
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC85" class="line" lang="c"> <span class="n" style="color: #333333;"><span class="idiff left addition" style="background-color: #c7f0d2;">encoded_upper</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">=</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">_mm_and_si128</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">(</span></span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">encoded_upper</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">,</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">_mm_set1_epi8</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">(</span></span><span class="mi" style="color: #009999;"><span class="idiff addition" style="background-color: #c7f0d2;">15</span></span><span class="p"><span class="idiff right addition" style="background-color: #c7f0d2;">)</span>);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="102" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="86" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
86
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC86" class="line" lang="c"> <span class="n" style="color: #333333;">__m128i</span> <span class="n" style="color: #333333;"><span class="idiff left addition" style="background-color: #c7f0d2;">encoded</span>_lower</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">_mm_<span class="idiff addition" style="background-color: #c7f0d2;">and_si128</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">(</span></span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">encoded</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">,</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">_mm_set1_epi8</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">(</span></span><span class="mi" style="color: #009999;"><span class="idiff addition" style="background-color: #c7f0d2;">15</span></span><span class="p"><span class="idiff right addition" style="background-color: #c7f0d2;">)</span>);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="102" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="87" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
87
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC87" class="line" lang="c"> <span class="n" style="color: #333333;">__m128i</span> <span class="n" style="color: #333333;"><span class="idiff left addition" style="background-color: #c7f0d2;">nucs</span>_upper</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">_mm_s<span class="idiff addition" style="background-color: #c7f0d2;">huffle_epi8</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">(</span></span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">nuc_lookup_vec</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">,</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333333;"><span class="idiff right addition" style="background-color: #c7f0d2;">encoded_upper</span></span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="102" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="88" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
88
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC88" class="line" lang="c"> <span class="n" style="color: #333333;">__m128i</span> <span class="n" style="color: #333333;"><span class="idiff left addition" style="background-color: #c7f0d2;">nucs_lower</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">=</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">_mm_shuffle_epi8</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">(</span></span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">nuc_lookup_vec</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">,</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333333;"><span class="idiff right addition" style="background-color: #c7f0d2;">encoded</span>_lower</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="102" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="89" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
89
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC89" class="line" lang="c"> <span class="n" style="color: #333333;">__m128i</span> <span class="n" style="color: #333333;">first_<span class="idiff left addition" style="background-color: #c7f0d2;">nucleotides</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">=</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">_mm_unpacklo_epi8</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">(</span></span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">nucs_upper</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">,</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333333;"><span class="idiff right addition" style="background-color: #c7f0d2;">nucs_lower</span></span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="102" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="90" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
90
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC90" class="line" lang="c"> <span class="n" style="color: #333333;">__m128i</span> <span class="n" style="color: #333333;"><span class="idiff left addition" style="background-color: #c7f0d2;">second</span>_nucleotides</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">_mm_<span class="idiff addition" style="background-color: #c7f0d2;">unpackhi</span>_epi8</span><span class="p">(</span><span class="n" style="color: #333333;">nuc<span class="idiff addition" style="background-color: #c7f0d2;">s_upper</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">,</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333333;"><span class="idiff right addition" style="background-color: #c7f0d2;">nucs_lower</span></span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="102" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
102
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<td class="new_line diff-line-num" data-linenumber="91" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
91
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC91" class="line" lang="c"> <span class="n" style="color: #333333;">_mm_storeu_si128</span><span class="p">((</span><span class="n" style="color: #333333;">__m128i</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333333;">dest_cursor</span><span class="p">,</span> <span class="n" style="color: #333333;">first_nucleotides</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="103" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
103
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<td class="new_line diff-line-num old" data-linenumber="92" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC103" class="line" lang="c"></span>
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<td class="old_line diff-line-num old" data-linenumber="104" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
104
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<td class="new_line diff-line-num old" data-linenumber="92" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC104" class="line" lang="c"> <span class="n" style="color: #333333;">__m128i</span> <span class="n" style="color: #333333;">second_upper</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">_mm_shuffle_epi8</span><span class="p">(</span><span class="n" style="color: #333333;">encoded</span><span class="p">,</span> <span class="n" style="color: #333333;">second_upper_shuffle</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="105" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
105
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<td class="new_line diff-line-num old" data-linenumber="92" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC105" class="line" lang="c"> <span class="n" style="color: #333333;">__m128i</span> <span class="n" style="color: #333333;">second_lower</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">_mm_shuffle_epi8</span><span class="p">(</span><span class="n" style="color: #333333;">encoded</span><span class="p">,</span> <span class="n" style="color: #333333;">second_lower_shuffle</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="106" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
106
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<td class="new_line diff-line-num old" data-linenumber="92" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC106" class="line" lang="c"> <span class="n" style="color: #333333;">__m128i</span> <span class="n" style="color: #333333;">shifted_second_upper</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">_mm_srli_epi64</span><span class="p">(</span><span class="n" style="color: #333333;">second_upper</span><span class="p">,</span> <span class="mi" style="color: #009999;">4</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="107" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
107
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<td class="new_line diff-line-num old" data-linenumber="92" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC107" class="line" lang="c"> <span class="n" style="color: #333333;">__m128i</span> <span class="n" style="color: #333333;">second_merged</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">_mm_or_si128</span><span class="p">(</span><span class="n" style="color: #333333;">shifted_second_upper</span><span class="p">,</span> <span class="n" style="color: #333333;">second_lower</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="108" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
108
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<td class="new_line diff-line-num old" data-linenumber="92" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC108" class="line" lang="c"> <span class="n" style="color: #333333;">__m128i</span> <span class="n" style="color: #333333;">second_indexes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">_mm_and_si128</span><span class="p">(</span><span class="n" style="color: #333333;">second_merged</span><span class="p">,</span> <span class="n" style="color: #333333;">_mm_set1_epi8</span><span class="p">(</span><span class="mi" style="color: #009999;">0</span><span class="n" style="color: #333333;">b1111</span><span class="p">));</span></span>
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<td class="old_line diff-line-num old" data-linenumber="109" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
109
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<td class="new_line diff-line-num old" data-linenumber="92" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC109" class="line" lang="c"> <span class="n" style="color: #333333;">__m128i</span> <span class="n" style="color: #333333;">second_nucleotides</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">_mm_shuffle_epi8</span><span class="p">(</span><span class="n" style="color: #333333;">nuc_lookup_vec</span><span class="p">,</span> <span class="n" style="color: #333333;">second_indexes</span><span class="p">);</span></span>
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110
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<td class="new_line diff-line-num" data-linenumber="92" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
92
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC92" class="line" lang="c"> <span class="n" style="color: #333333;">_mm_storeu_si128</span><span class="p">((</span><span class="n" style="color: #333333;">__m128i</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)(</span><span class="n" style="color: #333333;">dest_cursor</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #009999;">16</span><span class="p">),</span> <span class="n" style="color: #333333;">second_nucleotides</span><span class="p">);</span></span>
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111
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<td class="new_line diff-line-num old" data-linenumber="93" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC111" class="line" lang="c"></span>
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<td class="old_line diff-line-num" data-linenumber="112" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
112
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<td class="new_line diff-line-num" data-linenumber="93" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
93
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC93" class="line" lang="c"> <span class="n" style="color: #333333;">encoded_cursor</span> <span class="o" style="font-weight: 600;">+=</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333333;">__m128i</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="113" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
113
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<td class="new_line diff-line-num" data-linenumber="94" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
94
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC94" class="line" lang="c"> <span class="n" style="color: #333333;">dest_cursor</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #009999;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333333;">__m128i</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="114" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
114
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<td class="new_line diff-line-num" data-linenumber="95" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
95
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC95" class="line" lang="c"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="115" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
115
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<td class="new_line diff-line-num" data-linenumber="96" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
96
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC96" class="line" lang="c"> <span class="n" style="color: #333333;">decode_bam_sequence_default</span><span class="p">(</span><span class="n" style="color: #333333;">dest_cursor</span><span class="p">,</span> <span class="n" style="color: #333333;">encoded_cursor</span><span class="p">,</span> <span class="n" style="color: #333333;">dest_end_ptr</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333333;">dest_cursor</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="116" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
116
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<td class="new_line diff-line-num" data-linenumber="97" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
97
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC97" class="line" lang="c"><span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="117" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
117
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<td class="new_line diff-line-num" data-linenumber="98" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
98
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC98" class="line" lang="c"></span>
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<td class="old_line diff-line-num old" data-linenumber="118" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
118
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<td class="new_line diff-line-num old" data-linenumber="99" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC118" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="nf" style="color: #990000; font-weight: 600;">void</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333333;">decode_bam_sequence</span><span class="p">)(</span></span>
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<td class="old_line diff-line-num old" data-linenumber="119" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
119
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<td class="new_line diff-line-num old" data-linenumber="99" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC119" class="line" lang="c"> <span class="kt" style="color: #445588; font-weight: 600;">uint8_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333333;">dest</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #445588; font-weight: 600;">uint8_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333333;">encoded_sequence</span><span class="p">,</span> <span class="kt" style="color: #445588; font-weight: 600;">size_t</span> <span class="n" style="color: #333333;">length</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="120" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
120
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<td class="new_line diff-line-num old" data-linenumber="99" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC120" class="line" lang="c"></span>
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<td class="old_line diff-line-num old" data-linenumber="121" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
121
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<td class="new_line diff-line-num old" data-linenumber="99" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC121" class="line" lang="c"><span class="cm" style="color: #999988; font-style: italic;">/* Simple dispatcher function, updates the function pointer after testing the</span></span>
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<td class="old_line diff-line-num old" data-linenumber="122" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
122
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<td class="new_line diff-line-num old" data-linenumber="99" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC122" class="line" lang="c"><span class="cm" style="color: #999988; font-style: italic;"> CPU capabilities. After this, the dispatcher function is not needed anymore. */</span></span>
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<td class="old_line diff-line-num old" data-linenumber="123" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
123
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<td class="new_line diff-line-num old" data-linenumber="99" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC123" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #445588; font-weight: 600;">void</span> <span class="nf" style="color: #990000; font-weight: 600;">decode_bam_sequence_dispatch</span><span class="p">(</span></span>
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<td class="old_line diff-line-num old" data-linenumber="124" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
124
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<td class="new_line diff-line-num old" data-linenumber="99" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC124" class="line" lang="c"> <span class="kt" style="color: #445588; font-weight: 600;">uint8_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333333;">dest</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #445588; font-weight: 600;">uint8_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333333;">encoded_sequence</span><span class="p">,</span> <span class="kt" style="color: #445588; font-weight: 600;">size_t</span> <span class="n" style="color: #333333;">length</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="125" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="99" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
99
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC99" class="line" lang="c"><span class="cm" style="color: #999988; font-style: italic;">/* Constructor functions run at dynamic link time. This checks the CPU capabilities </span></span>
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<td class="old_line diff-line-num new" data-linenumber="125" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="100" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
100
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC100" class="line" lang="c"><span class="cm" style="color: #999988; font-style: italic;"> and updates the function pointer accordingly. */</span></span>
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<td class="old_line diff-line-num new" data-linenumber="125" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="101" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
101
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC101" class="line" lang="c"><span class="n" style="color: #333333;">__attribute__</span><span class="p">((</span><span class="n" style="color: #333333;">constructor</span><span class="p">))</span></span>
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<td class="old_line diff-line-num new" data-linenumber="125" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="102" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
102
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC102" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #445588; font-weight: 600;">void</span> <span class="nf" style="color: #990000; font-weight: 600;">decode_bam_sequence_dispatch</span><span class="p">(</span><span class="kt" style="color: #445588; font-weight: 600;">void</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="125" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
125
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<td class="new_line diff-line-num" data-linenumber="103" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
103
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC103" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333333;">__builtin_cpu_supports</span><span class="p">(</span><span class="s" style="color: #dd1144;">"ssse3"</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="126" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
126
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<td class="new_line diff-line-num" data-linenumber="104" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
104
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC104" class="line" lang="c"> <span class="n" style="color: #333333;">decode_bam_sequence</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">decode_bam_sequence_ssse3</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="127" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
127
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<td class="new_line diff-line-num" data-linenumber="105" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
105
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC105" class="line" lang="c"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="128" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
128
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<td class="new_line diff-line-num" data-linenumber="106" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
106
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC106" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="129" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
129
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<td class="new_line diff-line-num" data-linenumber="107" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
107
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC107" class="line" lang="c"> <span class="n" style="color: #333333;">decode_bam_sequence</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">decode_bam_sequence_default</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="130" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
130
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<td class="new_line diff-line-num" data-linenumber="108" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
108
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC108" class="line" lang="c"> <span class="p">}</span></span>
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<td class="old_line diff-line-num old" data-linenumber="131" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
131
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<td class="new_line diff-line-num old" data-linenumber="109" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC131" class="line" lang="c"> <span class="n" style="color: #333333;">decode_bam_sequence</span><span class="p">(</span><span class="n" style="color: #333333;">dest</span><span class="p">,</span> <span class="n" style="color: #333333;">encoded_sequence</span><span class="p">,</span> <span class="n" style="color: #333333;">length</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="132" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
132
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<td class="new_line diff-line-num old" data-linenumber="109" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC132" class="line" lang="c"><span class="p">}</span></span>
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<td class="old_line diff-line-num old" data-linenumber="133" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
133
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<td class="new_line diff-line-num old" data-linenumber="109" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC133" class="line" lang="c"></span>
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<td class="old_line diff-line-num old" data-linenumber="134" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
134
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<td class="new_line diff-line-num old" data-linenumber="109" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC134" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #445588; font-weight: 600;">void</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333333;">decode_bam_sequence</span><span class="p">)(</span></span>
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<td class="old_line diff-line-num old" data-linenumber="135" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
135
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<td class="new_line diff-line-num old" data-linenumber="109" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC135" class="line" lang="c"> <span class="kt" style="color: #445588; font-weight: 600;">uint8_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333333;">dest</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #445588; font-weight: 600;">uint8_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333333;">encoded_sequence</span><span class="p">,</span> <span class="kt" style="color: #445588; font-weight: 600;">size_t</span> <span class="n" style="color: #333333;">length</span></span>
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<td class="old_line diff-line-num old" data-linenumber="136" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
136
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<td class="new_line diff-line-num old" data-linenumber="109" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC136" class="line" lang="c"><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">decode_bam_sequence_dispatch</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="137" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
137
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<td class="new_line diff-line-num old" data-linenumber="109" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC137" class="line" lang="c"></span>
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<td class="old_line diff-line-num old" data-linenumber="138" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
138
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<td class="new_line diff-line-num old" data-linenumber="109" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC138" class="line" lang="c"><span class="cp" style="color: #999999; font-weight: 600;">#else</span></span>
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<td class="old_line diff-line-num old" data-linenumber="139" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
139
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<td class="new_line diff-line-num old" data-linenumber="109" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC139" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #445588; font-weight: 600;">void</span> <span class="nf" style="color: #990000; font-weight: 600;">decode_bam_sequence</span><span class="p">(</span><span class="kt" style="color: #445588; font-weight: 600;">uint8_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333333;">dest</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #445588; font-weight: 600;">uint8_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333333;">encoded_sequence</span><span class="p">,</span> <span class="kt" style="color: #445588; font-weight: 600;">size_t</span> <span class="n" style="color: #333333;">length</span><span class="p">)</span> </span>
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<td class="old_line diff-line-num old" data-linenumber="140" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
140
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<td class="new_line diff-line-num old" data-linenumber="109" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC140" class="line" lang="c"><span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="141" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
141
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC141" class="line" lang="c"> <span class="n" style="color: #333333;">decode_bam_sequence_default</span><span class="p">(</span><span class="n" style="color: #333333;">dest</span><span class="p">,</span> <span class="n" style="color: #333333;">encoded_sequence</span><span class="p">,</span> <span class="n" style="color: #333333;">length</span><span class="p">);</span></span>
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142
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109
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC109" class="line" lang="c"><span class="p">}</span></span>
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143
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110
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC110" class="line" lang="c"><span class="cp" style="color: #999999; font-weight: 600;">#endif </span></span>
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<a href="https://salsa.debian.org/med-team/python-dnaio/-/commit/40879644044aca1c849a2d9722d5d3acaa3d0f87#7fbd6a476804513c3f1fc7ab211e4080842865d6"><strong style="font-weight: 600;">tests/data/missing_quals.bam</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="803" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="803" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -803,3 +803,13 @@ class TestBamReader:</td>
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803
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<td class="new_line diff-line-num" data-linenumber="803" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
803
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC803" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333333;">pytest</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">raises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">NotImplementedError</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333333;">error</span><span class="p">:</span></span>
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804
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<td class="new_line diff-line-num" data-linenumber="804" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
804
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC804" class="line" lang="python"> <span class="nf" style="color: #990000; font-weight: 600;">next</span><span class="p">(</span><span class="n" style="color: #333333;">it</span><span class="p">)</span></span>
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805
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<td class="new_line diff-line-num" data-linenumber="805" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
805
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC805" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333333;">error</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">match</span><span class="p">(</span><span class="sh" style="color: #dd1144;">"</span><span class="s" style="color: #dd1144;">unmapped single reads</span><span class="sh" style="color: #dd1144;">"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="806" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
806
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC806" class="line" lang="python"></span>
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<td class="old_line diff-line-num new" data-linenumber="806" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
807
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC807" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #990000; font-weight: 600;">test_parse_bam_missing_quals</span><span class="p">(</span><span class="n" style="color: #333333;">self</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="808" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
808
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC808" class="line" lang="python"> <span class="n" style="color: #333333;">bam</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">TEST_DATA</span> <span class="o" style="font-weight: 600;">/</span> <span class="sh" style="color: #dd1144;">"</span><span class="s" style="color: #dd1144;">missing_quals.bam</span><span class="sh" style="color: #dd1144;">"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="809" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
809
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC809" class="line" lang="python"> <span class="n" style="color: #333333;">reader</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #445588; font-weight: 600;">BamReader</span><span class="p">(</span><span class="nf" style="color: #990000; font-weight: 600;">str</span><span class="p">(</span><span class="n" style="color: #333333;">bam</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="810" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
810
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC810" class="line" lang="python"> <span class="n" style="color: #333333;">records</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #990000; font-weight: 600;">list</span><span class="p">(</span><span class="n" style="color: #333333;">reader</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="811" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
811
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC811" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nf" style="color: #990000; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333333;">records</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #009999;">1</span></span>
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<td class="new_line diff-line-num new" data-linenumber="812" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
812
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC812" class="line" lang="python"> <span class="n" style="color: #333333;">record</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">records</span><span class="p">[</span><span class="mi" style="color: #009999;">0</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="813" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
813
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC813" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333333;">record</span><span class="p">.</span><span class="n" style="color: #333333;">sequence</span> <span class="o" style="font-weight: 600;">==</span> <span class="sh" style="color: #dd1144;">"</span><span class="s" style="color: #dd1144;">GATTACA</span><span class="sh" style="color: #dd1144;">"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="814" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
814
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC814" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"># Phred scores should default to 0 + 33 == ord('!') when missing.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="815" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
815
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC815" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333333;">record</span><span class="p">.</span><span class="n" style="color: #333333;">qualities</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999999;">None</span></span></pre></td>
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