tag:github.com,2008:https://github.com/prophyle/prophyle/releases 2024-04-21T15:27:20Z tag:github.com,2008:Repository/49076502/0.3.3.2 2024-04-21T15:29:30Z <h2>Changes</h2> <ul> <li>Fix compilation for M1 by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/karel-brinda/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/karel-brinda">@karel-brinda</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2255126808" data-permission-text="Title is private" data-url="https://github.com/prophyle/prophyle/issues/400" data-hovercard-type="pull_request" data-hovercard-url="/prophyle/prophyle/pull/400/hovercard" href="https://github.com/prophyle/prophyle/pull/400">#400</a></li> <li>Update dependencies</li> </ul> <h2>Full Changelog</h2> <p><a class="commit-link" href="https://github.com/prophyle/prophyle/compare/0.3.3.1...0.3.3.2"><tt>0.3.3.1...0.3.3.2</tt></a></p> karel-brinda tag:github.com,2008:Repository/49076502/0.3.3.1 2021-08-23T20:09:31Z <p>Update dependencies</p> karel-brinda tag:github.com,2008:Repository/49076502/0.3.3.0 2021-08-16T20:55:57Z <h1>New features:</h1> <ul> <li><code>prophyle footprint</code> for estimating the required memory footprint</li> </ul> <h1>Enhancements:</h1> <ul> <li>Integer ranks</li> <li>fastapath renamed to path</li> <li>Improved tests</li> <li>Refactoring</li> <li>Updated docs</li> <li>ln tag added to outputs</li> </ul> <h1>Closed issues</h1> <ul> <li>Unclassified reads are missing from the SAM output <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="336395777" data-permission-text="Title is private" data-url="https://github.com/prophyle/prophyle/issues/324" data-hovercard-type="issue" data-hovercard-url="/prophyle/prophyle/issues/324/hovercard" href="https://github.com/prophyle/prophyle/issues/324">#324</a></li> <li>Re-running finished decompression damages .bwt <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="405754877" data-permission-text="Title is private" data-url="https://github.com/prophyle/prophyle/issues/329" data-hovercard-type="issue" data-hovercard-url="/prophyle/prophyle/issues/329/hovercard" href="https://github.com/prophyle/prophyle/issues/329">#329</a></li> <li>Add prophyle footprint <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="334280588" data-permission-text="Title is private" data-url="https://github.com/prophyle/prophyle/issues/322" data-hovercard-type="issue" data-hovercard-url="/prophyle/prophyle/issues/322/hovercard" href="https://github.com/prophyle/prophyle/issues/322">#322</a></li> <li>Add the ln tag <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="315616153" data-permission-text="Title is private" data-url="https://github.com/prophyle/prophyle/issues/297" data-hovercard-type="issue" data-hovercard-url="/prophyle/prophyle/issues/297/hovercard" href="https://github.com/prophyle/prophyle/issues/297">#297</a></li> <li>propagation clean: Argument list too long <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="285338679" data-permission-text="Title is private" data-url="https://github.com/prophyle/prophyle/issues/292" data-hovercard-type="issue" data-hovercard-url="/prophyle/prophyle/issues/292/hovercard" href="https://github.com/prophyle/prophyle/issues/292">#292</a></li> </ul> karel-brinda tag:github.com,2008:Repository/49076502/0.3.2.0 2021-08-16T22:22:25Z <p>Fix many bugs and implement new features including</p> <ul> <li>Argument list too long (propagation) <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="320330405" data-permission-text="Title is private" data-url="https://github.com/prophyle/prophyle/issues/301" data-hovercard-type="issue" data-hovercard-url="/prophyle/prophyle/issues/301/hovercard" href="https://github.com/prophyle/prophyle/issues/301">#301</a></li> <li>prophyle decompress – "tar: could not chdir to 'database/sparc1_k18'" <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="323370491" data-permission-text="Title is private" data-url="https://github.com/prophyle/prophyle/issues/312" data-hovercard-type="issue" data-hovercard-url="/prophyle/prophyle/issues/312/hovercard" href="https://github.com/prophyle/prophyle/issues/312">#312</a></li> <li>No LCA computation in case of tie <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="323736688" data-permission-text="Title is private" data-url="https://github.com/prophyle/prophyle/issues/315" data-hovercard-type="issue" data-hovercard-url="/prophyle/prophyle/issues/315/hovercard" href="https://github.com/prophyle/prophyle/issues/315">#315</a></li> <li>prophyle_assignment: not enough values to unpack (expected 2, got 1) <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="328535021" data-permission-text="Title is private" data-url="https://github.com/prophyle/prophyle/issues/320" data-hovercard-type="issue" data-hovercard-url="/prophyle/prophyle/issues/320/hovercard" href="https://github.com/prophyle/prophyle/issues/320">#320</a></li> <li>RecursionError: maximum recursion depth exceeded while pickling an object <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="718700467" data-permission-text="Title is private" data-url="https://github.com/prophyle/prophyle/issues/337" data-hovercard-type="issue" data-hovercard-url="/prophyle/prophyle/issues/337/hovercard" href="https://github.com/prophyle/prophyle/issues/337">#337</a></li> <li>Error: /bin/bash: /bin/cat: Argument list too long <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="963142929" data-permission-text="Title is private" data-url="https://github.com/prophyle/prophyle/issues/350" data-hovercard-type="issue" data-hovercard-url="/prophyle/prophyle/issues/350/hovercard" href="https://github.com/prophyle/prophyle/issues/350">#350</a></li> <li>Add a param to stop after k-mer propagation <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="964051866" data-permission-text="Title is private" data-url="https://github.com/prophyle/prophyle/issues/353" data-hovercard-type="issue" data-hovercard-url="/prophyle/prophyle/issues/353/hovercard" href="https://github.com/prophyle/prophyle/issues/353">#353</a></li> </ul> karel-brinda tag:github.com,2008:Repository/49076502/0.3.1.0 2017-11-20T00:35:59Z <h2>Improvements</h2> <ul> <li>Download databases from Zenodo rather than from NCBI (in order to fix versions).</li> <li>Improve I/O error messages printed by <code>prophyle_assembler</code>.</li> <li>Improve ProPhyle code.</li> </ul> karel-brinda tag:github.com,2008:Repository/49076502/0.3.0.3 2017-11-20T00:35:26Z <h2>New</h2> <ul> <li>Add <code>make help</code> to print a list of commands for developers</li> <li>Add <code>make coverage</code> to compute code coverage</li> <li>Add <code>make pylint</code> to run Pylint</li> <li>Add a Code of Conduct</li> <li>Add <code>prophyle compile -F</code> for forcing a recompilation</li> </ul> <h2>Improvements</h2> <ul> <li>Specify recommended versions of dependencies for PyPI</li> </ul> karel-brinda tag:github.com,2008:Repository/49076502/0.3.0.2 2017-11-20T00:35:34Z <h2>Fixes</h2> <ul> <li>Fix the order of SAM headers in the output of <code>prophyle classify</code>.</li> </ul> karel-brinda tag:github.com,2008:Repository/49076502/0.3.0.1 2017-11-20T00:34:56Z <h2>New</h2> <ul> <li>Add <code>make submodules</code> to download submodules using <code>curl</code>.</li> </ul> <h2>Improvements</h2> <ul> <li>If submodules are missing from the repository, download them using <code>curl</code> during compilation.</li> </ul> karel-brinda tag:github.com,2008:Repository/49076502/0.3.0.0 2017-11-11T16:32:41Z <p>A major update. Rewritten assignment algorithm, improved tests, new classification parameters, and many fixed bugs.</p> <h2>New</h2> <ul> <li>Autodetect restarted search vs. rolling window from the index.</li> <li>Add revision &amp; commit info to <code>prophyle -v</code> (using git hooks).</li> <li>Add LCA options <code>-L</code> and <code>-X</code>, and an option to fully mimic Kraken (<code>-M</code> = <code>-m h1 -f kraken -L -X</code>).</li> <li>Add an internal system of passing additional parameters (using JSON).</li> <li>Add hf and cf tags to the SAM output.</li> <li>Add h2 and c2 as measures for assignments.</li> </ul> <h2>Improvements</h2> <ul> <li>Restructure and improve tests.</li> <li>Test ProPhyle both from the package and from the repository directory.</li> <li>Improve the master Makefile.</li> <li>Make ProPhyle less verbose (especially the compilation commands).</li> <li>Improve the Kraken-like format.</li> <li>Refactor &amp; optimize the assignment algorithm.</li> </ul> <h2>Fixes</h2> <ul> <li>Fix a FASTQ buffering bug in <code>prophyle_index</code> (loading entire read sets when used with Oxford Nanopore data).</li> <li>Fix LCA-related bugs in the Kraken-like mode.</li> <li>Fix many other minor bugs in entire package.</li> </ul> karel-brinda tag:github.com,2008:Repository/49076502/0.2.0 2017-07-22T22:29:03Z <p>Update docs</p> <p>Former-commit-id: <a class="commit-link" data-hovercard-type="commit" data-hovercard-url="https://github.com/prophyle/prophyle/commit/489d6a43157d7fe02b3abe0383cb09a5a8213e95/hovercard" href="https://github.com/prophyle/prophyle/commit/489d6a43157d7fe02b3abe0383cb09a5a8213e95"><tt>489d6a4</tt></a></p> karel-brinda