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Adds summary table to intro. See merge request machine-learning/modkit!45
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‎README.md

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A bioinformatics tool for working with modified bases from Oxford Nanopore. Specifically for converting modBAM
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to bedMethyl files using best practices, but also manipulating modBAM files and generating summary statistics.
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Detailed documentation and quick-start can be found in the [online docs](https://nanoporetech.github.io/modkit/).
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Detailed documentation and quick-start can be found in the [online documentation](https://nanoporetech.github.io/modkit/).
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## Installation
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| 13 | N<sub>canonical</sub> | See definitions above. | int |
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| 14 | N<sub>other_mod</sub> | See definitions above. | int |
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| 15 | N<sub>delete</sub> | See definitions above. | int |
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| 16 | N<sub>filtered</sub> | See definitions above. | int |
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| 16 | N<sub>fail</sub> | See definitions above. | int |
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| 17 | N<sub>diff</sub> | See definitions above. | int |
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| 18 | N<sub>nocall</sub> | See definitions above. | int |
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|--------|------------|------------------------------------------------------------------------------------------|-------|
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| 1 | base | canonical base with modification call | char |
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| 2 | code | base modification code, or `-` for canonical | char |
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| 3 | all_count | total number of calls for the modification code in column 2 | int |
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| 4 | all_frac | fraction of all calls for the modification in column 2 | float |
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| 5 | pass_count | total number of passing (confidence >= threshold) calls for the modification in column 2 | int |
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| 6 | pass_frac | fraction of passing (>= threshold) calls for the modification in column 2 | float |
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| 3 | pass_count | total number of passing (confidence >= threshold) calls for the modification in column 2 | int |
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| 4 | pass_frac | fraction of passing (>= threshold) calls for the modification in column 2 | float |
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| 5 | all_count | total number of calls for the modification code in column 2 | int |
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| 6 | all_frac | fraction of all calls for the modification in column 2 | float |
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‎book/src/intro_bedmethyl.md

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| 13 | N<sub>canonical</sub> | See definitions above. | int |
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| 14 | N<sub>other_mod</sub> | See definitions above. | int |
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| 15 | N<sub>delete</sub> | See definitions above. | int |
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| 16 | N<sub>filtered</sub> | See definitions above. | int |
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| 16 | N<sub>fail</sub> | See definitions above. | int |
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| 17 | N<sub>diff</sub> | See definitions above. | int |
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| 18 | N<sub>nocall</sub> | See definitions above. | int |
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‎book/src/intro_summary.md

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```
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The `pass_count` and `pass_frac` columns are the statistics for calls with confidence
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greater than or equal to the `pass_threshold` for that canonical base's calls. For more
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details on thresholds see [filtering base modification calls](./filtering.md).
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## Description of columns in `modkit summary`:
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### Totals table
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The lines of the totals table are prefixed with a `#` character.
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| row | name | description | type |
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|-----|-------------------------|-------------------------------------------------------------------------|--------|
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| 1 | bases | comma-separated list of canonical bases with modification calls. | str |
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| 2 | total_reads_used | total number of reads from which base modification calls were extracted | int |
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| 3+ | count_reads_{base} | total number of reads that contained base modifications for {base} | int |
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| 4+ | filter_threshold_{base} | filter threshold used for {base} | float |
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### Modification calls table
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The modification calls table follows immediately after the totals table.
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| column | name | description | type |
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|--------|------------|------------------------------------------------------------------------------------------|-------|
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| 1 | base | canonical base with modification call | char |
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| 2 | code | base modification code, or `-` for canonical | char |
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| 3 | pass_count | total number of passing (confidence >= threshold) calls for the modification in column 2 | int |
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| 4 | pass_frac | fraction of passing (>= threshold) calls for the modification in column 2 | float |
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| 5 | all_count | total number of calls for the modification code in column 2 | int |
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| 6 | all_frac | fraction of all calls for the modification in column 2 | float |
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For more details on thresholds see [filtering base modification calls](./filtering.md).
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By default `modkit summary` will only use ten thousand reads when generating the summary
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(or fewer if the modBAM has fewer than that). To use all of the reads in the modBAM set

‎docs/intro_bedmethyl.html

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<tr><td>13</td><td>N<sub>canonical</sub></td><td>See definitions above.</td><td>int</td></tr>
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<tr><td>14</td><td>N<sub>other_mod</sub></td><td>See definitions above.</td><td>int</td></tr>
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<tr><td>15</td><td>N<sub>delete</sub></td><td>See definitions above.</td><td>int</td></tr>
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<tr><td>16</td><td>N<sub>filtered</sub></td><td>See definitions above.</td><td>int</td></tr>
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<tr><td>16</td><td>N<sub>fail</sub></td><td>See definitions above.</td><td>int</td></tr>
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<tr><td>17</td><td>N<sub>diff</sub></td><td>See definitions above.</td><td>int</td></tr>
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<tr><td>18</td><td>N<sub>nocall</sub></td><td>See definitions above.</td><td>int</td></tr>
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</tbody></table>

‎docs/intro_summary.html

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</code></pre>
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<p>The <code>pass_count</code> and <code>pass_frac</code> columns are the statistics for calls with confidence
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greater than or equal to the <code>pass_threshold</code> for that canonical base's calls. For more
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details on thresholds see <a href="./filtering.html">filtering base modification calls</a>.</p>
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<h2 id="description-of-columns-in-modkit-summary"><a class="header" href="#description-of-columns-in-modkit-summary">Description of columns in <code>modkit summary</code>:</a></h2>
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<h3 id="totals-table"><a class="header" href="#totals-table">Totals table</a></h3>
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<p>The lines of the totals table are prefixed with a <code>#</code> character.</p>
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<div class="table-wrapper"><table><thead><tr><th>row</th><th>name</th><th>description</th><th>type</th></tr></thead><tbody>
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<tr><td>1</td><td>bases</td><td>comma-separated list of canonical bases with modification calls.</td><td>str</td></tr>
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<tr><td>2</td><td>total_reads_used</td><td>total number of reads from which base modification calls were extracted</td><td>int</td></tr>
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<tr><td>3+</td><td>count_reads_{base}</td><td>total number of reads that contained base modifications for {base}</td><td>int</td></tr>
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<tr><td>4+</td><td>filter_threshold_{base}</td><td>filter threshold used for {base}</td><td>float</td></tr>
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</tbody></table>
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</div>
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<h3 id="modification-calls-table"><a class="header" href="#modification-calls-table">Modification calls table</a></h3>
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<p>The modification calls table follows immediately after the totals table.</p>
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<div class="table-wrapper"><table><thead><tr><th>column</th><th>name</th><th>description</th><th>type</th></tr></thead><tbody>
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<tr><td>1</td><td>base</td><td>canonical base with modification call</td><td>char</td></tr>
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<tr><td>2</td><td>code</td><td>base modification code, or <code>-</code> for canonical</td><td>char</td></tr>
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<tr><td>3</td><td>pass_count</td><td>total number of passing (confidence &gt;= threshold) calls for the modification in column 2</td><td>int</td></tr>
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<tr><td>4</td><td>pass_frac</td><td>fraction of passing (&gt;= threshold) calls for the modification in column 2</td><td>float</td></tr>
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<tr><td>5</td><td>all_count</td><td>total number of calls for the modification code in column 2</td><td>int</td></tr>
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<tr><td>6</td><td>all_frac</td><td>fraction of all calls for the modification in column 2</td><td>float</td></tr>
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</tbody></table>
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</div>
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<p>For more details on thresholds see <a href="./filtering.html">filtering base modification calls</a>.</p>
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<p>By default <code>modkit summary</code> will only use ten thousand reads when generating the summary
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(or fewer if the modBAM has fewer than that). To use all of the reads in the modBAM set
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the <code>--no-sampling</code> flag.</p>

‎docs/print.html

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<tr><td>13</td><td>N<sub>canonical</sub></td><td>See definitions above.</td><td>int</td></tr>
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<tr><td>14</td><td>N<sub>other_mod</sub></td><td>See definitions above.</td><td>int</td></tr>
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<tr><td>15</td><td>N<sub>delete</sub></td><td>See definitions above.</td><td>int</td></tr>
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<tr><td>16</td><td>N<sub>filtered</sub></td><td>See definitions above.</td><td>int</td></tr>
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<tr><td>16</td><td>N<sub>fail</sub></td><td>See definitions above.</td><td>int</td></tr>
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<tr><td>17</td><td>N<sub>diff</sub></td><td>See definitions above.</td><td>int</td></tr>
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<tr><td>18</td><td>N<sub>nocall</sub></td><td>See definitions above.</td><td>int</td></tr>
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</tbody></table>
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</code></pre>
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<p>The <code>pass_count</code> and <code>pass_frac</code> columns are the statistics for calls with confidence
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greater than or equal to the <code>pass_threshold</code> for that canonical base's calls. For more
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details on thresholds see <a href="./filtering.html">filtering base modification calls</a>.</p>
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<h2 id="description-of-columns-in-modkit-summary"><a class="header" href="#description-of-columns-in-modkit-summary">Description of columns in <code>modkit summary</code>:</a></h2>
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<h3 id="totals-table"><a class="header" href="#totals-table">Totals table</a></h3>
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<p>The lines of the totals table are prefixed with a <code>#</code> character.</p>
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<div class="table-wrapper"><table><thead><tr><th>row</th><th>name</th><th>description</th><th>type</th></tr></thead><tbody>
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<tr><td>1</td><td>bases</td><td>comma-separated list of canonical bases with modification calls.</td><td>str</td></tr>
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<tr><td>2</td><td>total_reads_used</td><td>total number of reads from which base modification calls were extracted</td><td>int</td></tr>
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<tr><td>3+</td><td>count_reads_{base}</td><td>total number of reads that contained base modifications for {base}</td><td>int</td></tr>
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<tr><td>4+</td><td>filter_threshold_{base}</td><td>filter threshold used for {base}</td><td>float</td></tr>
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</tbody></table>
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</div>
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<h3 id="modification-calls-table"><a class="header" href="#modification-calls-table">Modification calls table</a></h3>
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<p>The modification calls table follows immediately after the totals table.</p>
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<div class="table-wrapper"><table><thead><tr><th>column</th><th>name</th><th>description</th><th>type</th></tr></thead><tbody>
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<tr><td>1</td><td>base</td><td>canonical base with modification call</td><td>char</td></tr>
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<tr><td>2</td><td>code</td><td>base modification code, or <code>-</code> for canonical</td><td>char</td></tr>
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<tr><td>3</td><td>pass_count</td><td>total number of passing (confidence &gt;= threshold) calls for the modification in column 2</td><td>int</td></tr>
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<tr><td>4</td><td>pass_frac</td><td>fraction of passing (&gt;= threshold) calls for the modification in column 2</td><td>float</td></tr>
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<tr><td>5</td><td>all_count</td><td>total number of calls for the modification code in column 2</td><td>int</td></tr>
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<tr><td>6</td><td>all_frac</td><td>fraction of all calls for the modification in column 2</td><td>float</td></tr>
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</tbody></table>
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</div>
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<p>For more details on thresholds see <a href="./filtering.html">filtering base modification calls</a>.</p>
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<p>By default <code>modkit summary</code> will only use ten thousand reads when generating the summary
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(or fewer if the modBAM has fewer than that). To use all of the reads in the modBAM set
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the <code>--no-sampling</code> flag.</p>

‎docs/searchindex.js

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