Closed BinglanLi closed 3 years ago
Do you want to request a feature or report a bug? bug
What is the current behavior? PharmCAT reporter does not have "-c" option.
If the current behavior is a bug, please provide the steps to reproduce and, if possible, your example input data via a Gist or similar. ~/jdk/jdk-14/bin/java -cp pharmcat-1.1.0-all.jar org.pharmgkb.pharmcat.reporter.Reporter -h usage: Reporter -h,--help print this message -j,--output-json optional, file path to write JSON data to -o,--output-file file path to write HTML report to -p,--phenotyper-file phenotyper output JSON file -t,--title optional, text to add to the report title -v,--verbose enable verbose output</p> </li> <li> <p><strong>What is the expected behavior?</strong></p> </li> </ul> <p>Reporter should have a <em>-c</em> option to take the JSON call file from the Named Allele Matcher. </p> <ul> <li> <p><strong>Please tell us about your environment:</strong></p> <ul> <li>PharmCAT Version: v1.1.0</li> <li>JDK Version: [ JDK8 | OpenJDK | etc ]: OpenJDK 14</li> <li>Environment: [ Windows | macOS | Linux distro | etc ] Linux x64</li> </ul> </li> <li> <p><strong>Other information</strong> (e.g. detailed explanation, stacktraces, related issues, suggestions how to fix, links for us to have context, e.g. stackoverflow, gitter, etc.)</p> </li> </ul> <p>Here is the screen shot of error message when running reporter. <img referrerpolicy="no-referrer" src="https://user-images.githubusercontent.com/17301572/137566293-f506b81e-e3f4-4915-8283-8e042e2ea84a.png" alt="image" /></p> </div> </div> <div class="comment"> <div class="user"> <a rel="noreferrer nofollow" target="_blank" href="https://github.com/whaleyr"><img src="https://avatars.githubusercontent.com/u/329004?v=4" />whaleyr</a> commented <strong> 3 years ago</strong> </div> <div class="markdown-body"> <p>I'm guessing you're saying the Reporter should have a <code>-c</code> option because it was in the wiki documentation. That was an error and I've updated the wiki to reflect the actual CLI flags for the Reporter. </p> <p>The Reporter can't actually take input straight from the NamedAlleleMatcher. It has to go through the Phenotyper first and then it can take the Phenotyper output as input. So either run the Phenotyper as a middle step or, what I prefer, just run the whole PharmCat tool and that way you can get all data and outputs.</p> </div> </div> <div class="comment"> <div class="user"> <a rel="noreferrer nofollow" target="_blank" href="https://github.com/BinglanLi"><img src="https://avatars.githubusercontent.com/u/17301572?v=4" />BinglanLi</a> commented <strong> 3 years ago</strong> </div> <div class="markdown-body"> <p>I missed the "-p" option. It's working. </p> </div> </div> <div class="page-bar-simple"> </div> <div class="footer"> <ul class="body"> <li>© <script> document.write(new Date().getFullYear()) </script> Githubissues.</li> <li>Githubissues is a development platform for aggregating issues.</li> </ul> </div> <script src="https://cdn.jsdelivr.net/npm/jquery@3.5.1/dist/jquery.min.js"></script> <script src="/githubissues/assets/js.js"></script> <script src="/githubissues/assets/markdown.js"></script> <script src="https://cdn.jsdelivr.net/gh/highlightjs/cdn-release@11.4.0/build/highlight.min.js"></script> <script src="https://cdn.jsdelivr.net/gh/highlightjs/cdn-release@11.4.0/build/languages/go.min.js"></script> <script> hljs.highlightAll(); </script> </body> </html>
Do you want to request a feature or report a bug? bug
What is the current behavior? PharmCAT reporter does not have "-c" option.
If the current behavior is a bug, please provide the steps to reproduce and, if possible, your example input data via a Gist or similar. ~/jdk/jdk-14/bin/java -cp pharmcat-1.1.0-all.jar org.pharmgkb.pharmcat.reporter.Reporter -h usage: Reporter -h,--help print this message -j,--output-json optional, file path to write JSON data
to
-o,--output-file file path to write HTML report to
-p,--phenotyper-file phenotyper output JSON file
-t,--title optional, text to add to the report
title
-v,--verbose enable verbose output</p>
</li>
<li>
<p><strong>What is the expected behavior?</strong></p>
</li>
</ul>
<p>Reporter should have a <em>-c</em> option to take the JSON call file from the Named Allele Matcher. </p>
<ul>
<li>
<p><strong>Please tell us about your environment:</strong></p>
<ul>
<li>PharmCAT Version: v1.1.0</li>
<li>JDK Version: [ JDK8 | OpenJDK | etc ]: OpenJDK 14</li>
<li>Environment: [ Windows | macOS | Linux distro | etc ] Linux x64</li>
</ul>
</li>
<li>
<p><strong>Other information</strong> (e.g. detailed explanation, stacktraces, related issues, suggestions how to fix, links for us to have context, e.g. stackoverflow, gitter, etc.)</p>
</li>
</ul>
<p>Here is the screen shot of error message when running reporter.
<img referrerpolicy="no-referrer" src="https://user-images.githubusercontent.com/17301572/137566293-f506b81e-e3f4-4915-8283-8e042e2ea84a.png" alt="image" /></p> </div>
</div>
<div class="comment">
<div class="user">
<a rel="noreferrer nofollow" target="_blank" href="https://github.com/whaleyr"><img src="https://avatars.githubusercontent.com/u/329004?v=4" />whaleyr</a>
commented
<strong> 3 years ago</strong> </div>
<div class="markdown-body">
<p>I'm guessing you're saying the Reporter should have a <code>-c</code> option because it was in the wiki documentation. That was an error and I've updated the wiki to reflect the actual CLI flags for the Reporter. </p>
<p>The Reporter can't actually take input straight from the NamedAlleleMatcher. It has to go through the Phenotyper first and then it can take the Phenotyper output as input. So either run the Phenotyper as a middle step or, what I prefer, just run the whole PharmCat tool and that way you can get all data and outputs.</p> </div>
</div>
<div class="comment">
<div class="user">
<a rel="noreferrer nofollow" target="_blank" href="https://github.com/BinglanLi"><img src="https://avatars.githubusercontent.com/u/17301572?v=4" />BinglanLi</a>
commented
<strong> 3 years ago</strong> </div>
<div class="markdown-body">
<p>I missed the "-p" option. It's working. </p> </div>
</div>
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