Merge branch 'ar/docs-typos' into 'master'

[docs] fix another broken link, update extract docs.

See merge request machine-learning/modkit!227

book/src/evaluate_motif.md

@@ -1,7 +1,7 @@
 # Evaluate a table of known motifs
 
 The `modkit search` command has an option to provide any number of known motifs with `--know-motif`.
-If you already have a list of candidate motifs (e.f. from a previous run of `modkit motif search`) you can check these motifs quickly against a bedMethyl table with `modkit motif evaluate`.
+However, if you already have a list of candidate motifs (e.g. from a previous run of `modkit motif search`) you can check these motifs quickly against a bedMethyl table with `modkit motif evaluate`.
 
 ```bash
 modkit motif evaluate -i ${bedmethyl} --known-motifs-table motifs.tsv -r ${ref}

book/src/intro_extract.md

@@ -88,10 +88,10 @@ For secondary and supplementary alignments, soft-clipped positions are not repea
 
 ### Extract a table of base modification probabilities from an aligned and indexed BAM 
 ```
-modkit extract full <input.bam> <output.tsv> 
+modkit extract full <input.bam> <output.tsv> [--bgzf]
 ```
 If the index `input.bam.bai` can be found, intervals along the aligned genome can be performed
-in parallel.
+in parallel. The optional `--bgzf` flag will emit compressed output.
 
 ### Extract a table from a region of a large modBAM
 The below example will extract reads from only chr20, and include reference sequence context
@@ -122,4 +122,4 @@ Use `--allow-non-primary` to get secondary and supplementary mappings in the out
 modkit extract calls <input.bam> <output.tsv> --allow-non-primary
 ```
 
-See the help string and/or [advanced_usage](./advanced_usage.md) for more details and [performace considerations](./perf_considerations.m) if you encounter issues with memory usage.
+See the help string and/or [advanced_usage](./advanced_usage.md) for more details and [performace considerations](./perf_considerations.md) if you encounter issues with memory usage.

docs/evaluate_motif.html

@@ -178,7 +178,7 @@ <h1 class="menu-title">Modkit</h1>
                     <main>
                         <h1 id="evaluate-a-table-of-known-motifs"><a class="header" href="#evaluate-a-table-of-known-motifs">Evaluate a table of known motifs</a></h1>
 <p>The <code>modkit search</code> command has an option to provide any number of known motifs with <code>--know-motif</code>.
-If you already have a list of candidate motifs (e.f. from a previous run of <code>modkit motif search</code>) you can check these motifs quickly against a bedMethyl table with <code>modkit motif evaluate</code>.</p>
+However, if you already have a list of candidate motifs (e.g. from a previous run of <code>modkit motif search</code>) you can check these motifs quickly against a bedMethyl table with <code>modkit motif evaluate</code>.</p>
 <pre><code class="language-bash">modkit motif evaluate -i ${bedmethyl} --known-motifs-table motifs.tsv -r ${ref}
 </code></pre>
 <p>Similarly, the search <a href="./intro_find_motifs.html#simple-description-of-the-search-algorithm">algorithm</a> can be run using known motifs as seeds:</p>

docs/intro_extract.html

@@ -255,10 +255,10 @@ <h2 id="note-on-non-primary-alignments"><a class="header" href="#note-on-non-pri
 For secondary and supplementary alignments, soft-clipped positions are not repeated. See <a href="./advanced_usage.html">advanced usage</a> for more details.</p>
 <h2 id="example-usages"><a class="header" href="#example-usages">Example usages:</a></h2>
 <h3 id="extract-a-table-of-base-modification-probabilities-from-an-aligned-and-indexed-bam"><a class="header" href="#extract-a-table-of-base-modification-probabilities-from-an-aligned-and-indexed-bam">Extract a table of base modification probabilities from an aligned and indexed BAM</a></h3>
-<pre><code>modkit extract full &lt;input.bam&gt; &lt;output.tsv&gt; 
+<pre><code>modkit extract full &lt;input.bam&gt; &lt;output.tsv&gt; [--bgzf]
 </code></pre>
 <p>If the index <code>input.bam.bai</code> can be found, intervals along the aligned genome can be performed
-in parallel.</p>
+in parallel. The optional <code>--bgzf</code> flag will emit compressed output.</p>
 <h3 id="extract-a-table-from-a-region-of-a-large-modbam"><a class="header" href="#extract-a-table-from-a-region-of-a-large-modbam">Extract a table from a region of a large modBAM</a></h3>
 <p>The below example will extract reads from only chr20, and include reference sequence context</p>
 <pre><code>modkit extract full &lt;intput.bam&gt; &lt;output.tsv&gt; --region chr20 --ref &lt;ref.fasta&gt;
@@ -276,7 +276,7 @@ <h3 id="extract-read-level-base-modification-calls"><a class="header" href="#ext
 <p>Use <code>--allow-non-primary</code> to get secondary and supplementary mappings in the output.</p>
 <pre><code>modkit extract calls &lt;input.bam&gt; &lt;output.tsv&gt; --allow-non-primary
 </code></pre>
-<p>See the help string and/or <a href="./advanced_usage.html">advanced_usage</a> for more details and <a href="./perf_considerations.m">performace considerations</a> if you encounter issues with memory usage.</p>
+<p>See the help string and/or <a href="./advanced_usage.html">advanced_usage</a> for more details and <a href="./perf_considerations.html">performace considerations</a> if you encounter issues with memory usage.</p>
 
                     </main>
 

docs/print.html

@@ -840,7 +840,7 @@ <h2 id="tuning-parameters-and---skip-search"><a class="header" href="#tuning-par
 <p>Also consider the additional steps in <a href="./perf_considerations.html#parallelism-in-find-motifs-when-to---skip-search">performance considerations.</a></p>
 <div style="break-before: page; page-break-before: always;"></div><h1 id="evaluate-a-table-of-known-motifs"><a class="header" href="#evaluate-a-table-of-known-motifs">Evaluate a table of known motifs</a></h1>
 <p>The <code>modkit search</code> command has an option to provide any number of known motifs with <code>--know-motif</code>.
-If you already have a list of candidate motifs (e.f. from a previous run of <code>modkit motif search</code>) you can check these motifs quickly against a bedMethyl table with <code>modkit motif evaluate</code>.</p>
+However, if you already have a list of candidate motifs (e.g. from a previous run of <code>modkit motif search</code>) you can check these motifs quickly against a bedMethyl table with <code>modkit motif evaluate</code>.</p>
 <pre><code class="language-bash">modkit motif evaluate -i ${bedmethyl} --known-motifs-table motifs.tsv -r ${ref}
 </code></pre>
 <p>Similarly, the search <a href="./intro_find_motifs.html#simple-description-of-the-search-algorithm">algorithm</a> can be run using known motifs as seeds:</p>
@@ -938,10 +938,10 @@ <h2 id="note-on-non-primary-alignments"><a class="header" href="#note-on-non-pri
 For secondary and supplementary alignments, soft-clipped positions are not repeated. See <a href="./advanced_usage.html">advanced usage</a> for more details.</p>
 <h2 id="example-usages-2"><a class="header" href="#example-usages-2">Example usages:</a></h2>
 <h3 id="extract-a-table-of-base-modification-probabilities-from-an-aligned-and-indexed-bam"><a class="header" href="#extract-a-table-of-base-modification-probabilities-from-an-aligned-and-indexed-bam">Extract a table of base modification probabilities from an aligned and indexed BAM</a></h3>
-<pre><code>modkit extract full &lt;input.bam&gt; &lt;output.tsv&gt; 
+<pre><code>modkit extract full &lt;input.bam&gt; &lt;output.tsv&gt; [--bgzf]
 </code></pre>
 <p>If the index <code>input.bam.bai</code> can be found, intervals along the aligned genome can be performed
-in parallel.</p>
+in parallel. The optional <code>--bgzf</code> flag will emit compressed output.</p>
 <h3 id="extract-a-table-from-a-region-of-a-large-modbam"><a class="header" href="#extract-a-table-from-a-region-of-a-large-modbam">Extract a table from a region of a large modBAM</a></h3>
 <p>The below example will extract reads from only chr20, and include reference sequence context</p>
 <pre><code>modkit extract full &lt;intput.bam&gt; &lt;output.tsv&gt; --region chr20 --ref &lt;ref.fasta&gt;
@@ -959,7 +959,7 @@ <h3 id="extract-read-level-base-modification-calls"><a class="header" href="#ext
 <p>Use <code>--allow-non-primary</code> to get secondary and supplementary mappings in the output.</p>
 <pre><code>modkit extract calls &lt;input.bam&gt; &lt;output.tsv&gt; --allow-non-primary
 </code></pre>
-<p>See the help string and/or <a href="./advanced_usage.html">advanced_usage</a> for more details and <a href="./perf_considerations.m">performace considerations</a> if you encounter issues with memory usage.</p>
+<p>See the help string and/or <a href="./advanced_usage.html">advanced_usage</a> for more details and <a href="./perf_considerations.html">performace considerations</a> if you encounter issues with memory usage.</p>
 <div style="break-before: page; page-break-before: always;"></div><h1 id="investigating-patterns-with-localise"><a class="header" href="#investigating-patterns-with-localise">Investigating patterns with localise</a></h1>
 <p>One a bedMethyl table has been created, <code>modkit localise</code> will use the pileup and calculate per-base modification aggregate information around genomic features of interest.
 For example, we can investigate base modification patterns around CTCF binding sites.</p>