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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/pbh5tools">Debian Med / pbh5tools</a>
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<h4>
Commits:
</h4>
<ul>
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<strong><a href="https://salsa.debian.org/med-team/pbh5tools/commit/7385d38eff8bb426d02e5718b46004192f0fe164">7385d38e</a></strong>
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<span>by Andreas Tille</span>
<i>at 2019-12-07T08:10:00Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.8.0+git20181212.9fa8fc4+dfsg</pre>
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<h4>1 changed file:</h4>
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<a href="#1bbcd8980c541f52998ccf56da078edd2ca6a2d0">
doc/index.rst
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<h4>Changes:</h4>
<li id="1bbcd8980c541f52998ccf56da078edd2ca6a2d0">
<a href="https://salsa.debian.org/med-team/pbh5tools/commit/7385d38eff8bb426d02e5718b46004192f0fe164#1bbcd8980c541f52998ccf56da078edd2ca6a2d0"><strong>doc/index.rst</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -28,6 +28,14 @@ To install ``pbh5tools``, run the following command from the ``pbh5tools`` root</td>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"> python setup.py install</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">If you do not have `root` or `sudo` permissions, you can install locally by: </span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">1. Installing pysam, numpy, Cython, and h5py to your home directory. </span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> pip install --user --upgrade numpy h5py pysam cython</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">2. Running </span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> python setup.py install --user</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext">####################</span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext">Tool: bash5tools.py</span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext">####################</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -80,10 +88,10 @@ Usage</td>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="plaintext">Examples</span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="plaintext">--------</span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="plaintext">Extracting all <span class="idiff left right">Raw</span> reads from ``input.bas.h5`` without any filtering</span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="plaintext">and exporting to <span class="idiff left right">FASTA (``myreads.fasta``)</span>: ::</span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext">Extracting all <span class="idiff left right">subreads</span> reads from ``input.bas.h5`` without any filtering</span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext">and exporting to <span class="idiff left right">a FASTA file named ``myreads.fasta``</span>: ::</span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="plaintext"> python bash5tools.py <span class="idiff left right">input.bas.h5 --outFilePrefix myreads --outType fasta --readType Raw</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext"> python bash5tools.py <span class="idiff left right">--outFilePrefix myreads --outType fasta --readType subreads input.bas.h5</span></span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="plaintext">Extracting all CCS reads from ``input.bas.h5`` that have read lengths</span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="plaintext">larger than 100 and exporting to FASTQ (``myreads.fastq``): ::</span>
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