https://curiouscoding.nl/tags/bitpacking/Recent content in Bitpacking on CuriousCodingHugoenSun, 03 Sep 2023 00:00:00 +0200https://curiouscoding.nl/posts/bitpal/Sun, 03 Sep 2023 00:00:00 +0200https://curiouscoding.nl/posts/bitpal/<div class="ox-hugo-toc toc"> <div class="heading">Table of Contents</div> <ul> <li><a href="#problem" >Problem</a></li> <li><a href="#input" >Input</a></li> <li><a href="#example" >Example</a></li> <li><a href="#discussion" >Discussion</a></li> <li><a href="#found-the-bug" >Found the bug</a></li> <li><a href="#outlook" >Outlook</a></li> </ul> </div> <!--endtoc--> <p>The supplement (<a href="https://oup.silverchair-cdn.com/oup/backfile/Content_public/Journal/bioinformatics/30/22/10.1093_bioinformatics_btu507/3/bioinformatics_30_22_3166_s1.zip?Expires=1695376479&amp;Signature=vroWHrpg-P0tvOPcafVy~gh6mhZ-AZ8kj6lHr1DH7byZGTK2sy8chti7hDiWdbtGx6onKv94EAI5odd~GMBMG0GNXxfp1bZ~7ItGeNCXp0tosJpArez7Yo~PuKT77nJpgQYo5rabbkJ6qtvP3-V-41oznQ~Zh9Tl~GNLvjLo~5vq0D1wa4PMmqhc-C0zcEeh8ybqEK7hQdyvoxreWppOTZFIHIJwmZOSOeXBWM0fQhcPnM9ZU8cEsqAI64WuWt1AJgmDOPDTBVzQHmHpsl01F4Jt8Hf2gvDYwhmoM7t4U~qCIGFr4raran~hzr-eD2vhwexQhpC7e1U2~N2lMC7e7w__&amp;Key-Pair-Id=APKAIE5G5CRDK6RD3PGA" class="external-link" target="_blank" rel="noopener">download</a>) of the Loving, Hernandez, and Benson (<a href="#citeproc_bib_item_1">2014</a>) paper introduces a \(15\) operation version of Myers (<a href="#citeproc_bib_item_2">1999</a>) bitpacking algorithm, which uses \(16\) operations when modified for edit distance.</p> <p>I tried implementing it, but it seems to have a bug that I will describe below. The fix is <a href="#found-the-bug" >here</a>.</p> <h2 id="problem"> Problem <a class="heading-link" href="#problem"> <i class="fa-solid fa-link" aria-hidden="true" title="Link to heading"></i> <span class="sr-only">Link to heading</span> </a> </h2> <p>To recap, this algorithm solves the unit-cost edit distance problem by using bitpacking to compute a \(1\times w\) at a time. As input, it takes</p>