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<a href="https://github.com/broadinstitute/viral-ngs/commit/<a class=hub.com/broadinstitute/viral-ngs/commit/<a class="double-link" href="https://git"><a class=hub.com/broadinstitute/viral-ngs/commit/<a class="double-link" href="https://git"><a class=hub.com/broadinstitute/viral-ngs/commit/0c51acb62c45696f237554620a3a4d3332dda7e4">0c51acb62<a href="https://github.com/broadinstitute/viral-ngs/commit/0c51acb62c45696f237554620a3a4d3332dda7e4">&lt;a href=&quot;https://github.com/broadinstitute/viral-ngs/commit/0c51acb62c45696f237554620a3a4d3332dda7e4&quot;&gt;&amp;lt;a href=&amp;quot;https://github.com/broadinstitute/viral-ngs/commit/0c51acb62c45696f237554620a3a4d3332dda7e4&amp;quot;&amp;gt;&amp;amp;quot;&amp;amp;gt;binned coverage plot option in align_and_plot (#957)

* fixed indentation, repeated code in plot_coverage

* added binning for large plots, on by default

* added command line and pipe option for binning (now off by default)

* moved binLargePlots argument to parser_plot_coverage_common

* makes sample name field in plot_coverage optional to allow running in bulk (gets sample name from reads_unmapped_bam)

* hopefully fixed syntax

* hopefully fixed syntax

* syntax debugging: fixed string equality in if statement, commented out code following if statement

* moved wdl code out of the command block--hopefully this fixes it

* moved use of reads_unmapped_bam to AFTER it&amp;amp;#39;s initialized, oops

* Revert &amp;amp;quot;moved use of reads_unmapped_bam to AFTER it&amp;amp;#39;s initialized, oops&amp;amp;quot;

This reverts commit &amp;lt;/a&amp;gt;&amp;lt;a class=&amp;quot;double-link&amp;quot; href=&amp;quot;https://github.com/broadinstitute/viral-ngs/commit/&amp;lt;a class=&amp;quot;double-link&amp;quot; href=&quot;https://github.com/broadinstitute/viral-ngs/commit/a820ab2a132c942a98e6b0a653a22ad8cf540b0f&quot;&gt;a820ab2a1&lt;/a&gt;&quot;&gt;a820ab2a1&lt;/a&gt;&lt;a href=&quot;https://github.com/broadinstitute/viral-ngs/commit/0c51acb62c45696f237554620a3a4d3332dda7e4&quot;&gt;.

* Revert &amp;quot;moved wdl code out of the command block--hopefully this fixes it&amp;quot;

This reverts commit &lt;/a&gt;&lt;a class=&quot;double-link&quot; href=&quot;https://github.com/broadinstitute/viral-ngs/commit/&lt;a class=&quot;double-link&quot; href=&quot;https://github.com/broadinstitute/viral-ngs/commit/4317d21f466a924c005fb3e6020ecc8634f5ca8b">4317d21f4</a>">4317d21f4</a><a href="https://github.com/broadinstitute/viral-ngs/commit/0c51acb62c45696f237554620a3a4d3332dda7e4">.

* Revert &quot;syntax debugging: fixed string equality in if statement, commented out code following if statement&quot;

This reverts commit </a><a class="double-link" href="https://github.com/broadinstitute/viral-ngs/commit/<a class="double-link" href="https://github.com/broadinstitute/viral-ngs/commit/a2b590b75d277a728b0f0f4afdd7f23cd9914e94">a2b590b75">a2b590b75.

* Revert "hopefully fixed syntax"

This revert... (continued)