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4 changes: 2 additions & 2 deletions docs/coverm-cluster.html
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<div class="cover-card table-cell table-middle">
<span class="author_name">coverm cluster usage</span>
<span class="author_bio mbm">Ben Woodcroft, Centre for Microbiome Research, Queensland University of Technology</span>
<span class="author_bio mbm">2020-12-11 (coverm 0.6.0)</span>
<span class="author_bio mbm">2021-02-25 (coverm 0.6.1)</span>
</div>
</div>
</div>
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<article class="post-content">
<div id="name" class="section level1">
<h1>NAME</h1>
<p>coverm cluster - Cluster genome FASTA files by average nucleotide identity (version 0.6.0)</p>
<p>coverm cluster - Cluster genome FASTA files by average nucleotide identity (version 0.6.1)</p>
</div>
<div id="synopsis" class="section level1">
<h1>SYNOPSIS</h1>
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25 changes: 13 additions & 12 deletions docs/coverm-contig.html
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<div class="cover-card table-cell table-middle">
<span class="author_name">coverm contig usage</span>
<span class="author_bio mbm">Ben Woodcroft, Centre for Microbiome Research, Queensland University of Technology</span>
<span class="author_bio mbm">2020-12-11 (coverm 0.6.0)</span>
<span class="author_bio mbm">2021-02-25 (coverm 0.6.1)</span>
</div>
</div>
</div>
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<li><a href="#coverage-calculation-options">COVERAGE CALCULATION OPTIONS</a></li>
<li><a href="#output">OUTPUT</a></li>
<li><a href="#general-options">GENERAL OPTIONS</a></li>
<li><a href="#frequently-asked-questions">FREQUENTLY ASKED QUESTIONS</a></li>
<li><a href="#frequently-asked-questions-faq">FREQUENTLY ASKED QUESTIONS (FAQ)</a></li>
<li><a href="#exit-status">EXIT STATUS</a></li>
<li><a href="#examples">EXAMPLES</a></li>
<li><a href="#author">AUTHOR</a></li>
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<article class="post-content">
<div id="name" class="section level1">
<h1>NAME</h1>
<p>coverm contig - Calculate read coverage per-contig (version 0.6.0)</p>
<p>coverm contig - Calculate read coverage per-contig (version 0.6.1)</p>
</div>
<div id="synopsis" class="section level1">
<h1>SYNOPSIS</h1>
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<!-- -->
<dl>
<dt><strong>--min-read-percent-identity</strong> <em>FLOAT</em></dt>
<dd><p>Exclude reads by overall percent identity e.g. 0.95 for 95%. [default: <code>0.0</code>]</p>
<dd><p>Exclude reads by overall percent identity e.g. 95 for 95%. [default: <code>0</code>]</p>
</dd>
</dl>
<!-- -->
<dl>
<dt><strong>--min-read-aligned-percent</strong> <em>FLOAT</em></dt>
<dd><p>Exclude reads by percent aligned bases e.g. 0.95 means 95% of the read&#39;s bases must be aligned. [default: <code>0.0</code>]</p>
<dd><p>Exclude reads by percent aligned bases e.g. 95 means 95% of the read&#39;s bases must be aligned. [default: <code>0</code>]</p>
</dd>
</dl>
<!-- -->
Expand All @@ -241,13 +241,13 @@ <h1>ALIGNMENT THRESHOLDING</h1>
<!-- -->
<dl>
<dt><strong>--min-read-percent-identity-pair</strong> <em>FLOAT</em></dt>
<dd><p>Exclude pairs by overall percent identity e.g. 0.95 for 95%. Implies --proper-pairs-only. [default: <code>0.0</code>]</p>
<dd><p>Exclude pairs by overall percent identity e.g. 95 for 95%. Implies --proper-pairs-only. [default: <code>0</code>]</p>
</dd>
</dl>
<!-- -->
<dl>
<dt><strong>--min-read-aligned-percent-pair</strong> <em>FLOAT</em></dt>
<dd><p>Exclude reads by percent aligned bases e.g. 0.95 means 95% of the read&#39;s bases must be aligned. Implies --proper-pairs-only. [default: <code>0.0</code>]</p>
<dd><p>Exclude reads by percent aligned bases e.g. 95 means 95% of the read&#39;s bases must be aligned. Implies --proper-pairs-only. [default: <code>0</code>]</p>
</dd>
</dl>
<!-- -->
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</table>
<dl>
<dt><strong>--min-covered-fraction</strong> <em>FRACTION</em></dt>
<dd><p>Genomes with less coverage than this reported as having zero coverage. [default: <code>0.10</code>]</p>
<dd><p>Genomes with less coverage than this reported as having zero coverage. [default: <code>10</code>]</p>
</dd>
</dl>
<!-- -->
Expand All @@ -335,13 +335,13 @@ <h1>COVERAGE CALCULATION OPTIONS</h1>
<!-- -->
<dl>
<dt><strong>--trim-min</strong> <em>FRACTION</em></dt>
<dd><p>Remove this smallest fraction of positions when calculating trimmed_mean [default: <code>0.05</code>]</p>
<dd><p>Remove this smallest fraction of positions when calculating trimmed_mean [default: <code>5</code>]</p>
</dd>
</dl>
<!-- -->
<dl>
<dt><strong>--trim-max</strong> <em>FRACTION</em></dt>
<dd><p>Maximum fraction for trimmed_mean calculations [default: <code>0.95</code>]</p>
<dd><p>Maximum fraction for trimmed_mean calculations [default: <code>95</code>]</p>
</dd>
</dl>
</div>
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</dd>
</dl>
</div>
<div id="frequently-asked-questions" class="section level1">
<h1>FREQUENTLY ASKED QUESTIONS</h1>
<div id="frequently-asked-questions-faq" class="section level1">
<h1>FREQUENTLY ASKED QUESTIONS (FAQ)</h1>
<p><strong>Can the temporary directory used be changed?</strong> CoverM makes use of the system temporary directory (often <code>/tmp</code>) to store intermediate files. This can cause problems if the amount of storage available there is small or used by many programs. To fix, set the <code>TMPDIR</code> environment variable e.g. to set it to use the current directory: <code>TMPDIR=. coverm genome &lt;etc&gt;</code></p>
<p><strong>For thresholding arguments e.g. --dereplication-ani and --min-read-percent-identity, should a percentage (e.g 97%) or fraction (e.g. 0.97) be specified?</strong> Either is fine, CoverM determines which is being used by virtue of being less than or greater than 1.</p>
</div>
<div id="exit-status" class="section level1">
<h1>EXIT STATUS</h1>
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21 changes: 11 additions & 10 deletions docs/coverm-filter.html
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<div class="cover-card table-cell table-middle">
<span class="author_name">coverm filter usage</span>
<span class="author_bio mbm">Ben Woodcroft, Centre for Microbiome Research, Queensland University of Technology</span>
<span class="author_bio mbm">2020-12-11 (coverm 0.6.0)</span>
<span class="author_bio mbm">2021-02-25 (coverm 0.6.1)</span>
</div>
</div>
</div>
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<li><a href="#flags">FLAGS</a></li>
<li><a href="#options">OPTIONS</a></li>
<li><a href="#alignment-thresholding">ALIGNMENT THRESHOLDING</a></li>
<li><a href="#frequently-asked-questions">FREQUENTLY ASKED QUESTIONS</a></li>
<li><a href="#frequently-asked-questions-faq">FREQUENTLY ASKED QUESTIONS (FAQ)</a></li>
<li><a href="#exit-status">EXIT STATUS</a></li>
<li><a href="#examples">EXAMPLES</a></li>
<li><a href="#author">AUTHOR</a></li>
Expand All @@ -90,7 +90,7 @@
<article class="post-content">
<div id="name" class="section level1">
<h1>NAME</h1>
<p>coverm filter - Threshold alignments with insufficient identity (version 0.6.0)</p>
<p>coverm filter - Threshold alignments with insufficient identity (version 0.6.1)</p>
</div>
<div id="synopsis" class="section level1">
<h1>SYNOPSIS</h1>
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<!-- -->
<dl>
<dt><strong>--min-read-percent-identity</strong> <em>FLOAT</em></dt>
<dd><p>Exclude reads by overall percent identity e.g. 0.95 for 95%. [default: <code>0.0</code>]</p>
<dd><p>Exclude reads by overall percent identity e.g. 95 for 95%. [default: <code>0</code>]</p>
</dd>
</dl>
<!-- -->
<dl>
<dt><strong>--min-read-aligned-percent</strong> <em>FLOAT</em></dt>
<dd><p>Exclude reads by percent aligned bases e.g. 0.95 means 95% of the read&#39;s bases must be aligned. [default: <code>0.0</code>]</p>
<dd><p>Exclude reads by percent aligned bases e.g. 95 means 95% of the read&#39;s bases must be aligned. [default: <code>0</code>]</p>
</dd>
</dl>
<!-- -->
Expand All @@ -186,13 +186,13 @@ <h1>ALIGNMENT THRESHOLDING</h1>
<!-- -->
<dl>
<dt><strong>--min-read-percent-identity-pair</strong> <em>FLOAT</em></dt>
<dd><p>Exclude pairs by overall percent identity e.g. 0.95 for 95%. Implies --proper-pairs-only. [default: <code>0.0</code>]</p>
<dd><p>Exclude pairs by overall percent identity e.g. 95 for 95%. Implies --proper-pairs-only. [default: <code>0</code>]</p>
</dd>
</dl>
<!-- -->
<dl>
<dt><strong>--min-read-aligned-percent-pair</strong> <em>FLOAT</em></dt>
<dd><p>Exclude reads by percent aligned bases e.g. 0.95 means 95% of the read&#39;s bases must be aligned. Implies --proper-pairs-only. [default: <code>0.0</code>]</p>
<dd><p>Exclude reads by percent aligned bases e.g. 95 means 95% of the read&#39;s bases must be aligned. Implies --proper-pairs-only. [default: <code>0</code>]</p>
</dd>
</dl>
<!-- -->
Expand All @@ -208,9 +208,10 @@ <h1>ALIGNMENT THRESHOLDING</h1>
</dd>
</dl>
</div>
<div id="frequently-asked-questions" class="section level1">
<h1>FREQUENTLY ASKED QUESTIONS</h1>
<div id="frequently-asked-questions-faq" class="section level1">
<h1>FREQUENTLY ASKED QUESTIONS (FAQ)</h1>
<p><strong>Can the temporary directory used be changed?</strong> CoverM makes use of the system temporary directory (often <code>/tmp</code>) to store intermediate files. This can cause problems if the amount of storage available there is small or used by many programs. To fix, set the <code>TMPDIR</code> environment variable e.g. to set it to use the current directory: <code>TMPDIR=. coverm genome &lt;etc&gt;</code></p>
<p><strong>For thresholding arguments e.g. --dereplication-ani and --min-read-percent-identity, should a percentage (e.g 97%) or fraction (e.g. 0.97) be specified?</strong> Either is fine, CoverM determines which is being used by virtue of being less than or greater than 1.</p>
</div>
<div id="exit-status" class="section level1">
<h1>EXIT STATUS</h1>
Expand Down Expand Up @@ -239,7 +240,7 @@ <h1>EXAMPLES</h1>
<dd><p><strong>$ coverm filter --bam-files input.bam --output-bam filtered.bam --min-read-aligned-length 50</strong></p>
</dd>
<dt>Filter inverse: Keep alignments that have &lt;95% alignment identity and those which do map at all. Note that the output BAM file will likely records that are still mapped, but align with &lt; 95% identity. Use 16 threads for output compression</dt>
<dd><p><strong>$ coverm filter -b input.bam -o inverse_filtered.bam --inverse --min-read-percent-identity 0.95 --threads 16</strong></p>
<dd><p><strong>$ coverm filter -b input.bam -o inverse_filtered.bam --inverse --min-read-percent-identity 95 --threads 16</strong></p>
</dd>
</dl>
</div>
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25 changes: 13 additions & 12 deletions docs/coverm-genome.html
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<div class="cover-card table-cell table-middle">
<span class="author_name">coverm genome usage</span>
<span class="author_bio mbm">Ben Woodcroft, Centre for Microbiome Research, Queensland University of Technology</span>
<span class="author_bio mbm">2020-12-11 (coverm 0.6.0)</span>
<span class="author_bio mbm">2021-02-25 (coverm 0.6.1)</span>
</div>
</div>
</div>
Expand All @@ -85,7 +85,7 @@
<li><a href="#coverage-calculation-options">COVERAGE CALCULATION OPTIONS</a></li>
<li><a href="#output">OUTPUT</a></li>
<li><a href="#general-options">GENERAL OPTIONS</a></li>
<li><a href="#frequently-asked-questions">FREQUENTLY ASKED QUESTIONS</a></li>
<li><a href="#frequently-asked-questions-faq">FREQUENTLY ASKED QUESTIONS (FAQ)</a></li>
<li><a href="#exit-status">EXIT STATUS</a></li>
<li><a href="#examples">EXAMPLES</a></li>
<li><a href="#author">AUTHOR</a></li>
Expand All @@ -96,7 +96,7 @@
<article class="post-content">
<div id="name" class="section level1">
<h1>NAME</h1>
<p>coverm genome - Calculate read coverage per-genome (version 0.6.0)</p>
<p>coverm genome - Calculate read coverage per-genome (version 0.6.1)</p>
</div>
<div id="synopsis" class="section level1">
<h1>SYNOPSIS</h1>
Expand Down Expand Up @@ -386,13 +386,13 @@ <h1>ALIGNMENT THRESHOLDING</h1>
<!-- -->
<dl>
<dt><strong>--min-read-percent-identity</strong> <em>FLOAT</em></dt>
<dd><p>Exclude reads by overall percent identity e.g. 0.95 for 95%. [default: <code>0.0</code>]</p>
<dd><p>Exclude reads by overall percent identity e.g. 95 for 95%. [default: <code>0</code>]</p>
</dd>
</dl>
<!-- -->
<dl>
<dt><strong>--min-read-aligned-percent</strong> <em>FLOAT</em></dt>
<dd><p>Exclude reads by percent aligned bases e.g. 0.95 means 95% of the read&#39;s bases must be aligned. [default: <code>0.0</code>]</p>
<dd><p>Exclude reads by percent aligned bases e.g. 95 means 95% of the read&#39;s bases must be aligned. [default: <code>0</code>]</p>
</dd>
</dl>
<!-- -->
Expand All @@ -404,13 +404,13 @@ <h1>ALIGNMENT THRESHOLDING</h1>
<!-- -->
<dl>
<dt><strong>--min-read-percent-identity-pair</strong> <em>FLOAT</em></dt>
<dd><p>Exclude pairs by overall percent identity e.g. 0.95 for 95%. Implies --proper-pairs-only. [default: <code>0.0</code>]</p>
<dd><p>Exclude pairs by overall percent identity e.g. 95 for 95%. Implies --proper-pairs-only. [default: <code>0</code>]</p>
</dd>
</dl>
<!-- -->
<dl>
<dt><strong>--min-read-aligned-percent-pair</strong> <em>FLOAT</em></dt>
<dd><p>Exclude reads by percent aligned bases e.g. 0.95 means 95% of the read&#39;s bases must be aligned. Implies --proper-pairs-only. [default: <code>0.0</code>]</p>
<dd><p>Exclude reads by percent aligned bases e.g. 95 means 95% of the read&#39;s bases must be aligned. Implies --proper-pairs-only. [default: <code>0</code>]</p>
</dd>
</dl>
<!-- -->
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</table>
<dl>
<dt><strong>--min-covered-fraction</strong> <em>FRACTION</em></dt>
<dd><p>Genomes with less coverage than this reported as having zero coverage. [default: <code>0.10</code>]</p>
<dd><p>Genomes with less coverage than this reported as having zero coverage. [default: <code>10</code>]</p>
</dd>
</dl>
<!-- -->
Expand All @@ -498,13 +498,13 @@ <h1>COVERAGE CALCULATION OPTIONS</h1>
<!-- -->
<dl>
<dt><strong>--trim-min</strong> <em>FRACTION</em></dt>
<dd><p>Remove this smallest fraction of positions when calculating trimmed_mean [default: <code>0.05</code>]</p>
<dd><p>Remove this smallest fraction of positions when calculating trimmed_mean [default: <code>5</code>]</p>
</dd>
</dl>
<!-- -->
<dl>
<dt><strong>--trim-max</strong> <em>FRACTION</em></dt>
<dd><p>Maximum fraction for trimmed_mean calculations [default: <code>0.95</code>]</p>
<dd><p>Maximum fraction for trimmed_mean calculations [default: <code>95</code>]</p>
</dd>
</dl>
</div>
Expand Down Expand Up @@ -578,9 +578,10 @@ <h1>GENERAL OPTIONS</h1>
</dd>
</dl>
</div>
<div id="frequently-asked-questions" class="section level1">
<h1>FREQUENTLY ASKED QUESTIONS</h1>
<div id="frequently-asked-questions-faq" class="section level1">
<h1>FREQUENTLY ASKED QUESTIONS (FAQ)</h1>
<p><strong>Can the temporary directory used be changed?</strong> CoverM makes use of the system temporary directory (often <code>/tmp</code>) to store intermediate files. This can cause problems if the amount of storage available there is small or used by many programs. To fix, set the <code>TMPDIR</code> environment variable e.g. to set it to use the current directory: <code>TMPDIR=. coverm genome &lt;etc&gt;</code></p>
<p><strong>For thresholding arguments e.g. --dereplication-ani and --min-read-percent-identity, should a percentage (e.g 97%) or fraction (e.g. 0.97) be specified?</strong> Either is fine, CoverM determines which is being used by virtue of being less than or greater than 1.</p>
</div>
<div id="exit-status" class="section level1">
<h1>EXIT STATUS</h1>
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11 changes: 6 additions & 5 deletions docs/coverm-make.html
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<div class="cover-card table-cell table-middle">
<span class="author_name">coverm make usage</span>
<span class="author_bio mbm">Ben Woodcroft, Centre for Microbiome Research, Queensland University of Technology</span>
<span class="author_bio mbm">2020-12-11 (coverm 0.6.0)</span>
<span class="author_bio mbm">2021-02-25 (coverm 0.6.1)</span>
</div>
</div>
</div>
Expand All @@ -81,7 +81,7 @@
<li><a href="#mapping-algorithm-options">MAPPING ALGORITHM OPTIONS</a></li>
<li><a href="#output">OUTPUT</a></li>
<li><a href="#general-options">GENERAL OPTIONS</a></li>
<li><a href="#frequently-asked-questions">FREQUENTLY ASKED QUESTIONS</a></li>
<li><a href="#frequently-asked-questions-faq">FREQUENTLY ASKED QUESTIONS (FAQ)</a></li>
<li><a href="#exit-status">EXIT STATUS</a></li>
<li><a href="#examples">EXAMPLES</a></li>
<li><a href="#author">AUTHOR</a></li>
Expand All @@ -92,7 +92,7 @@
<article class="post-content">
<div id="name" class="section level1">
<h1>NAME</h1>
<p>coverm make - Generate BAM files through mapping (version: 0.6.0)</p>
<p>coverm make - Generate BAM files through mapping (version: 0.6.1)</p>
</div>
<div id="synopsis" class="section level1">
<h1>SYNOPSIS</h1>
Expand Down Expand Up @@ -246,9 +246,10 @@ <h1>GENERAL OPTIONS</h1>
</dd>
</dl>
</div>
<div id="frequently-asked-questions" class="section level1">
<h1>FREQUENTLY ASKED QUESTIONS</h1>
<div id="frequently-asked-questions-faq" class="section level1">
<h1>FREQUENTLY ASKED QUESTIONS (FAQ)</h1>
<p><strong>Can the temporary directory used be changed?</strong> CoverM makes use of the system temporary directory (often <code>/tmp</code>) to store intermediate files. This can cause problems if the amount of storage available there is small or used by many programs. To fix, set the <code>TMPDIR</code> environment variable e.g. to set it to use the current directory: <code>TMPDIR=. coverm genome &lt;etc&gt;</code></p>
<p><strong>For thresholding arguments e.g. --dereplication-ani and --min-read-percent-identity, should a percentage (e.g 97%) or fraction (e.g. 0.97) be specified?</strong> Either is fine, CoverM determines which is being used by virtue of being less than or greater than 1.</p>
</div>
<div id="exit-status" class="section level1">
<h1>EXIT STATUS</h1>
Expand Down

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