https://sourceforge.net/p/pb-jelly/blog/2014/07/pbsuite-v14714/Recent changes to PBSuite v14.7.14enMon, 14 Jul 2014 20:10:32 -0000https://sourceforge.net/p/pb-jelly/blog/2014/07/pbsuite-v14714/<div class="markdown_content"><p>This version has a few minor bug-fixes in PBJelly, and functionality extension in PBHoney.</p> <p>Below are details from the CHANGELOG.txt</p> <div class="codehilite"><pre><span class="n">Honey</span><span class="p">.</span><span class="n">py</span> <span class="n">force</span> <span class="n">Added</span> <span class="n">parser</span> <span class="n">helpers</span> <span class="k">for</span> <span class="n">the</span> <span class="n">Force</span> <span class="n">output</span> <span class="n">format</span> <span class="n">as</span> <span class="n">well</span> <span class="n">as</span> <span class="n">a</span> <span class="err">'</span><span class="n">genotyper</span><span class="err">'</span> <span class="n">Improved</span> <span class="n">spot</span> <span class="n">forcing</span> <span class="n">by</span> <span class="n">chaninging</span> <span class="o">--</span><span class="n">minIns</span> <span class="n">to</span> <span class="o">--</span><span class="n">minErr</span><span class="p">.</span> <span class="n">Now</span> <span class="err">'</span><span class="n">twilight</span><span class="err">'</span> <span class="n">deletions</span> <span class="n">aren</span><span class="err">'</span><span class="n">t</span> <span class="n">incorrectly</span> <span class="n">forced</span> <span class="n">Added</span> <span class="o">--</span><span class="n">bedPE</span> <span class="n">Support</span> <span class="n">which</span> <span class="n">includes</span> <span class="n">a</span> <span class="n">couple</span> <span class="n">of</span> <span class="n">Bed</span> <span class="n">Objects</span><span class="p">...</span> <span class="n">which</span> <span class="n">probably</span> <span class="n">need</span> <span class="n">to</span> <span class="n">be</span> <span class="n">moved</span> <span class="n">to</span> <span class="n">utils</span><span class="o">/</span><span class="n">FileHandlers</span><span class="p">.</span><span class="n">py</span> <span class="n">recallSpots</span><span class="p">.</span><span class="n">py</span> <span class="n">Fixed</span> <span class="n">the</span> <span class="n">code</span> <span class="n">so</span> <span class="n">it</span> <span class="n">should</span> <span class="n">actually</span> <span class="n">work</span> <span class="n">HSpots</span><span class="p">.</span><span class="n">py</span> <span class="n">minor</span> <span class="n">code</span> <span class="n">cleaning</span> <span class="n">Jelly</span><span class="p">.</span><span class="n">py</span> <span class="n">output</span> <span class="n">Fixed</span> <span class="n">lower</span><span class="o">-</span><span class="n">casing</span> <span class="n">of</span> <span class="n">PBJelly</span> <span class="n">added</span> <span class="n">sequence</span> <span class="n">Added</span> <span class="n">trim</span> <span class="n">information</span> <span class="n">to</span> <span class="n">debugging</span> <span class="n">log</span> <span class="n">Fixed</span> <span class="err">'</span><span class="n">mySpanScore</span><span class="err">'</span> <span class="n">bug</span> <span class="n">Jelly</span><span class="p">.</span><span class="n">py</span> <span class="n">Added</span> <span class="p">.</span><span class="n">fasta</span><span class="o">/</span><span class="p">.</span><span class="n">fastq</span> <span class="n">extension</span> <span class="n">checking</span> <span class="k">for</span> <span class="n">inputs</span> <span class="n">in</span> <span class="n">Protocol</span> <span class="n">Jelly</span><span class="p">.</span><span class="n">py</span> <span class="n">collection</span> <span class="n">Added</span> <span class="n">safer</span> <span class="p">.</span><span class="n">fasta</span><span class="o">/</span><span class="p">.</span><span class="n">fastq</span> <span class="n">parser</span> <span class="n">choosing</span> <span class="n">Utils</span> <span class="n">quickN50</span><span class="p">.</span><span class="n">py</span> <span class="o">-</span> <span class="n">Made</span> <span class="n">the</span> <span class="n">output</span> <span class="n">report</span> <span class="n">more</span> <span class="n">attractive</span> <span class="n">FileHandlers</span><span class="p">.</span><span class="n">py</span> <span class="o">-</span> <span class="n">Added</span> <span class="n">to</span> <span class="n">lower</span><span class="o">/</span><span class="n">upper</span> <span class="n">methods</span> </pre></div> </div>Adam EnglishMon, 14 Jul 2014 20:10:32 -0000https://sourceforge.net3eb9b1f8cb27fdb0e5c9d9a493fb7af649eb3109