tag:github.com,2008:https://github.com/mlin/spVCF/releasesRelease notes from spVCF2023-10-29T00:54:40Ztag:github.com,2008:Repository/138694727/v1.3.22023-10-29T01:05:32Zv1.3.2<p><code>--with-missing-fields</code>: fill missing ref AD with DP,0</p>mlintag:github.com,2008:Repository/138694727/v1.3.12023-10-02T08:24:26Zv1.3.1<p><code>--with-missing-fields</code>: pad AD & PL to the expected vector length (with missing values) for biallelic sites</p>mlintag:github.com,2008:Repository/138694727/v1.3.02023-06-04T04:17:12Zv1.3.0<ul>
<li>Add <code>spvcf decode --with-missing-fields</code> flag to fill in all trailing FORMAT fields, even when their values are missing.</li>
<li>Update htslib & libdeflate versions</li>
</ul>mlintag:github.com,2008:Repository/138694727/v1.2.02022-01-07T09:14:22Zv1.2.0<ul>
<li>Fix omission of QC field(s) when DP isn't present (<a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1093323376" data-permission-text="Title is private" data-url="https://github.com/mlin/spVCF/issues/26" data-hovercard-type="issue" data-hovercard-url="/mlin/spVCF/issues/26/hovercard" href="https://github.com/mlin/spVCF/issues/26">#26</a> <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/RussellTaylor/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/RussellTaylor">@RussellTaylor</a>)</li>
<li>Update htslib and libdeflate versions</li>
<li>Executable target architecture advanced to Haswell (from Ivy Bridge)</li>
<li><a href="https://github.com/mlin/spVCF/pkgs/container/spvcf">Published Docker image</a></li>
<li>Modernize <a href="https://github.com/mlin/spVCF/blob/main/spvcf.wdl">spvcf.wdl</a></li>
</ul>mlintag:github.com,2008:Repository/138694727/v1.1.02020-12-27T07:34:54Zv1.1.0<ul>
<li>Update the linked htslib version</li>
<li>Modernize WDL wrappers</li>
<li>Minor speed improvements</li>
</ul>mlintag:github.com,2008:Repository/138694727/v1.0.02020-12-27T07:33:38Zv1.0.0 🍾<p>User can increase (or decrease) the resolution of DP rounding during QC squeezing, using <code>-r</code>/<code>--resolution</code></p>mlintag:github.com,2008:Repository/138694727/202012262020-12-27T07:38:11Z20201226No content.mlintag:github.com,2008:Repository/138694727/v0.7.02019-03-14T05:44:53Zrelease candidate<ul>
<li><code>spvcf encode</code>: perform QC squeezing by default (opt-out)</li>
<li>rewrite header e.g. <code>##fileformat=VCF4.2</code> to <code>##fileformat=spVCFvx.y.z-gabcdef;VCF4.2</code> and back</li>
<li>error message if input stream needs decompression</li>
<li>warning message if input stream doesn't start with expected <code>##fileformat</code></li>
<li>htslib 1.9</li>
</ul>mlintag:github.com,2008:Repository/138694727/v0.6.02018-10-02T06:01:37ZDon't quote-encode cells whose genotypes aren't reference-identical or non-called<p>This spec change ensures that all <em>non-reference</em> genotypes on a spVCF row can be read without referring to any previous row, a significant convenience in exchange for a negligible size increase (as the affected case, a run of non-reference genotypes with exactly repeated QC values down a column, is extremely rare).</p>mlintag:github.com,2008:Repository/138694727/v0.5.02018-08-29T08:36:13Zv0.5.0: Multithreaded encoder (#13)<p>Multithreaded encoder (<a class="issue-link js-issue-link" href="https://github.com/mlin/spVCF/pull/13">#13</a>)</p>
<p>The encoder can run multithreaded by buffering batches of input lines and processing each batch in a worker thread. In favorable circumstances this yields higher throughput than the default single-threaded approach, but there is a trade-off of greatly increased memory usage and copying. Activated with -t,--threads.</p>mlin