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fix(route): get correct item link #17278

Merged
merged 1 commit into from
Oct 26, 2024
Merged

fix(route): get correct item link #17278

merged 1 commit into from
Oct 26, 2024

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x1e5c
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@x1e5c x1e5c commented Oct 24, 2024 •
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Involved Issue / 该 PR 相关 Issue

Close #

Example for the Proposed Route(s) / 路由地址示例

/rsshub/transform/html/https%3A%2F%2Fllwslc.github.io%2Fgrammar-club%2Fcontent%2FPreface.html/title%3Dgrammar-club%26item%3D%20header%20%3E%20div.links%20%3E%20nav%20%3E%20div%20%26itemLink%3Da
/rsshub/transform/html/https%3A%2F%2Fbionumpy.github.io%2Fbionumpy%2Fmenu.html/itemLink%3Da

New RSS Route Checklist / 新 RSS 路由检查表

  • New Route / 新的路由
  • Anti-bot or rate limit / 反爬/频率限制
    • If yes, do your code reflect this sign? / 如果有, 是否有对应的措施?
  • Date and time / 日期和时间
    • Parsed / 可以解析
    • Correct time zone / 时区正确
  • New package added / 添加了新的包
  • Puppeteer

Note / 说明

When the href link inside the element is a relative link, the original handling would obtain an incorrect full link

This is the official documentation for numpy https://numpy.org/doc/stable/user/index.html, where most a tags have relative links. Here is the code effect before and after modification based on this site

item href `${new URL(url).origin}${link}` (new URL(link, url)).href
whatisnumpy.html https://numpy.orgwhatisnumpy.html https://numpy.org/doc/stable/user/whatisnumpy.html
../reference/index.html#reference https://numpy.org../reference/index.html#reference https://numpy.org/doc/stable/reference/index.html#reference

@x1e5c
get correct item link
51ac689 
When the `href` link inside the element is a relative link, the original handling would obtain an incorrect full link
@github-actions github-actions bot added Route Auto: Route Test Skipped PR involves no routes labels Oct 24, 2024
@x1e5c x1e5c changed the title get correct item link fix(route): get correct item link Oct 24, 2024
TonyRL
TonyRL reviewed Oct 24, 2024
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Please do provide an example for testing

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x1e5c commented Oct 25, 2024

@TonyRL

Please do provide an example for testing

This is the official documentation for numpy https://numpy.org/doc/stable/user/index.html, where most a tags have relative links. Here is the code effect before and after modification based on this site

item href `${new URL(url).origin}${link}` (new URL(link, url)).href
whatisnumpy.html https://numpy.orgwhatisnumpy.html https://numpy.org/doc/stable/user/whatisnumpy.html
../reference/index.html#reference https://numpy.org../reference/index.html#reference https://numpy.org/doc/stable/reference/index.html#reference

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TonyRL commented Oct 25, 2024

Please fill in the example in the PR template.

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TonyRL commented Oct 25, 2024 •
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I should make it clearer next time.

Please fill in the Example for the Proposed Route(s) / 路由地址示例 in the PR template for testing instead of skipping it.

@github-actions github-actions bot added the Auto: Route Test Complete Auto route test has finished on given PR label Oct 26, 2024
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Successfully generated as following:

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HTTPError: Response code 503 (Service Unavailable)

Error Message:<br/>FetchError: [GET] &quot;https://wechat2rss.xlab.app/posts/list/&quot;: 404 Not Found
Route: /rsshub/transform/html/:url/:routeParams
Full Route: /rsshub/transform/html/https%3A%2F%2Fwechat2rss.xlab.app%2Fposts%2Flist%2F/item=div[class%3D&#39;post-content&#39;] p a
Node Version: v22.10.0
Git Hash: 53452663
http://localhost:1200/rsshub/transform/html/https%3A%2F%2Fbionumpy.github.io%2Fbionumpy%2Fmenu.html/itemLink%3Da - Success ✔️ 
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        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/tutorials/subsetting_bed.html&quot;&gt;Getting read pileup inside peaks (intervals)&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/tutorials/fastqc.html&quot;&gt;FastQC-like quality-checking of FASTQ files&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/tutorials/gc_content.html&quot;&gt;Computing GC content inside genes&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/tutorials/position_weight_matrix.html&quot;&gt;Position Weight Matrix&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/tutorials/set_of_sequences.html&quot;&gt;Simulating sequence datasets&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/tutorials/similarity_measures.html&quot;&gt;Computing the similarity between two BED-files&lt;/a&gt;&lt;/li&gt;
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        &lt;p class=&quot;caption&quot; role=&quot;heading&quot;&gt;&lt;span class=&quot;caption-text&quot;&gt;Interoperability&lt;/span&gt;&lt;/p&gt;
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        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/source/broadcastable_functions.html&quot;&gt;Broadcastable Functions&lt;/a&gt;&lt;/li&gt;
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        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/developer_guide.html&quot;&gt;Developer guide&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/manuscript/index.html&quot;&gt;BioNumPy manuscript&lt;/a&gt;&lt;/li&gt;
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        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/introduction.html&quot;&gt;Getting started with BioNumPy in 10 minutes&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/using_bionumpy_in_your_existing_project.html&quot;&gt;Using BioNumPy in your existing project&lt;/a&gt;&lt;/li&gt;
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        &lt;p class=&quot;caption&quot; role=&quot;heading&quot;&gt;&lt;span class=&quot;caption-text&quot;&gt;Tutorials&lt;/span&gt;&lt;/p&gt;
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        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/tutorials/fastq_filtering.html&quot;&gt;Filtering FASTQ reads&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/tutorials/bam_handling.html&quot;&gt;Working with BAM-files&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/tutorials/subsetting_bed.html&quot;&gt;Getting read pileup inside peaks (intervals)&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/tutorials/fastqc.html&quot;&gt;FastQC-like quality-checking of FASTQ files&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/tutorials/gc_content.html&quot;&gt;Computing GC content inside genes&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/tutorials/position_weight_matrix.html&quot;&gt;Position Weight Matrix&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/tutorials/set_of_sequences.html&quot;&gt;Simulating sequence datasets&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/tutorials/similarity_measures.html&quot;&gt;Computing the similarity between two BED-files&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/tutorials/extracting_kmers_around_snps.html&quot;&gt;Extracting kmers around snps&lt;/a&gt;&lt;/li&gt;
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        &lt;p class=&quot;caption&quot; role=&quot;heading&quot;&gt;&lt;span class=&quot;caption-text&quot;&gt;Interoperability&lt;/span&gt;&lt;/p&gt;
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        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/interoperability/numpy_operations.html&quot;&gt;Numpy Interoperability&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/interoperability/working_with_biopython.html&quot;&gt;Using BioNumPy with Biopython&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/interoperability/pandas.html&quot;&gt;Pandas Interoperability&lt;/a&gt;&lt;/li&gt;
        &lt;/ul&gt;
        &lt;/div&gt;
        &lt;div class=&quot;toctree-wrapper compound&quot;&gt;
        &lt;p class=&quot;caption&quot; role=&quot;heading&quot;&gt;&lt;span class=&quot;caption-text&quot;&gt;BioNumPy Concepts&lt;/span&gt;&lt;/p&gt;
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        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/source/reading_files.html&quot;&gt;Reading files&lt;/a&gt;&lt;ul&gt;
        &lt;li class=&quot;toctree-l2&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/source/reading_files.html#method-1-reading-all-your-data-at-once&quot;&gt;Method 1: Reading all your data at once&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l2&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/source/reading_files.html#method-2-reading-a-single-chunk-from-a-large-file&quot;&gt;Method 2: Reading a single chunk from a large file&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l2&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/source/reading_files.html#method-3-reading-whole-file-as-a-stream-of-chunks&quot;&gt;Method 3: Reading whole file as a stream of chunks&lt;/a&gt;&lt;/li&gt;
        &lt;/ul&gt;
        &lt;/li&gt;
        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/source/encoding.html&quot;&gt;Encodings&lt;/a&gt;&lt;ul&gt;
        &lt;li class=&quot;toctree-l2&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/source/encoding.html#encoding-data-using-a-specific-encoding&quot;&gt;Encoding data using a specific encoding&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l2&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/source/encoding.html#supported-encodings&quot;&gt;Supported encodings&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l2&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/source/encoding.html#when-having-already-encoded-data-advanced-usage&quot;&gt;When having already encoded data (advanced usage)&lt;/a&gt;&lt;/li&gt;
        &lt;/ul&gt;
        &lt;/li&gt;
        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/source/supported_file_formats.html&quot;&gt;Supported file formats&lt;/a&gt;&lt;ul&gt;
        &lt;li class=&quot;toctree-l2&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/source/supported_file_formats.html#example&quot;&gt;Example&lt;/a&gt;&lt;/li&gt;
        &lt;/ul&gt;
        &lt;/li&gt;
        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/source/supported_file_formats.html#reading-a-new-file-format&quot;&gt;Reading a new file format&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/source/sequences.html&quot;&gt;Sequences&lt;/a&gt;&lt;ul&gt;
        &lt;li class=&quot;toctree-l2&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/source/sequences.html#encodedarray&quot;&gt;&lt;cite&gt;EncodedArray&lt;/cite&gt;&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l2&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/source/sequences.html#encodedraggedarray&quot;&gt;&lt;cite&gt;EncodedRaggedArray&lt;/cite&gt;&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l2&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/source/sequences.html#absolute-basics-of-encodedraggedarray&quot;&gt;Absolute basics of &lt;cite&gt;EncodedRaggedArray&lt;/cite&gt;&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l2&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/source/sequences.html#reading-sequences-from-file&quot;&gt;Reading sequences from file&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l2&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/source/sequences.html#functions-workin-on-sequences&quot;&gt;Functions workin on sequences&lt;/a&gt;&lt;/li&gt;
        &lt;/ul&gt;
        &lt;/li&gt;
        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/source/intervals.html&quot;&gt;Intervals&lt;/a&gt;&lt;ul&gt;
        &lt;li class=&quot;toctree-l2&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/source/intervals.html#independent-operations&quot;&gt;Independent Operations&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l2&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/source/intervals.html#operations-with-dependencies&quot;&gt;Operations with dependencies&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l2&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/source/intervals.html#genomic-intervals&quot;&gt;Genomic Intervals&lt;/a&gt;&lt;/li&gt;
        &lt;/ul&gt;
        &lt;/li&gt;
        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/source/multiple_data_sources.html&quot;&gt;Working with Multiple Files/Data Sources&lt;/a&gt;&lt;ul&gt;
        &lt;li class=&quot;toctree-l2&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/source/multiple_data_sources.html#sort-order&quot;&gt;Sort Order&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l2&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/source/multiple_data_sources.html#two-indexed-files&quot;&gt;Two Indexed Files&lt;/a&gt;&lt;/li&gt;
        &lt;/ul&gt;
        &lt;/li&gt;
        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/source/broadcastable_functions.html&quot;&gt;Broadcastable Functions&lt;/a&gt;&lt;ul&gt;
        &lt;li class=&quot;toctree-l2&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/source/broadcastable_functions.html#elementwise-broadcasting-in-numpy&quot;&gt;Elementwise broadcasting in NumPy&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l2&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/source/broadcastable_functions.html#vectorwise-broadcasting&quot;&gt;Vectorwise broadcasting&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l2&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/source/broadcastable_functions.html#sequence-broadcasting&quot;&gt;Sequence broadcasting&lt;/a&gt;&lt;/li&gt;
        &lt;/ul&gt;
        &lt;/li&gt;
        &lt;/ul&gt;
        &lt;/div&gt;
        &lt;div class=&quot;toctree-wrapper compound&quot;&gt;
        &lt;p class=&quot;caption&quot; role=&quot;heading&quot;&gt;&lt;span class=&quot;caption-text&quot;&gt;API documentation&lt;/span&gt;&lt;/p&gt;
        &lt;ul&gt;
        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/bnpdataclass.html&quot;&gt;BnpDataclass&lt;/a&gt;&lt;ul&gt;
        &lt;li class=&quot;toctree-l2&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/bnpdataclass.html#api-documentation&quot;&gt;API documentation&lt;/a&gt;&lt;ul&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/bnpdataclass.html#bionumpy.bnpdataclass.bnpdataclass&quot;&gt;&lt;code class=&quot;docutils literal notranslate&quot;&gt;&lt;span class=&quot;pre&quot;&gt;bnpdataclass()&lt;/span&gt;&lt;/code&gt;&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/bnpdataclass.html#bionumpy.bnpdataclass.replace&quot;&gt;&lt;code class=&quot;docutils literal notranslate&quot;&gt;&lt;span class=&quot;pre&quot;&gt;replace()&lt;/span&gt;&lt;/code&gt;&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/bnpdataclass.html#bionumpy.bnpdataclass.make_dataclass&quot;&gt;&lt;code class=&quot;docutils literal notranslate&quot;&gt;&lt;span class=&quot;pre&quot;&gt;make_dataclass()&lt;/span&gt;&lt;/code&gt;&lt;/a&gt;&lt;/li&gt;
        &lt;/ul&gt;
        &lt;/li&gt;
        &lt;/ul&gt;
        &lt;/li&gt;
        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/genome_arithmetics.html&quot;&gt;Genome arithmetics&lt;/a&gt;&lt;ul&gt;
        &lt;li class=&quot;toctree-l2&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/genome_arithmetics.html#api-documentation&quot;&gt;API documentation&lt;/a&gt;&lt;ul&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/genome_arithmetics.html#bionumpy.arithmetics.forbes&quot;&gt;&lt;code class=&quot;docutils literal notranslate&quot;&gt;&lt;span class=&quot;pre&quot;&gt;forbes()&lt;/span&gt;&lt;/code&gt;&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/genome_arithmetics.html#bionumpy.arithmetics.jaccard&quot;&gt;&lt;code class=&quot;docutils literal notranslate&quot;&gt;&lt;span class=&quot;pre&quot;&gt;jaccard()&lt;/span&gt;&lt;/code&gt;&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/genome_arithmetics.html#bionumpy.arithmetics.sort_intervals&quot;&gt;&lt;code class=&quot;docutils literal notranslate&quot;&gt;&lt;span class=&quot;pre&quot;&gt;sort_intervals()&lt;/span&gt;&lt;/code&gt;&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/genome_arithmetics.html#bionumpy.arithmetics.merge_intervals&quot;&gt;&lt;code class=&quot;docutils literal notranslate&quot;&gt;&lt;span class=&quot;pre&quot;&gt;merge_intervals()&lt;/span&gt;&lt;/code&gt;&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/genome_arithmetics.html#bionumpy.arithmetics.get_pileup&quot;&gt;&lt;code class=&quot;docutils literal notranslate&quot;&gt;&lt;span class=&quot;pre&quot;&gt;get_pileup()&lt;/span&gt;&lt;/code&gt;&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/genome_arithmetics.html#bionumpy.arithmetics.get_boolean_mask&quot;&gt;&lt;code class=&quot;docutils literal notranslate&quot;&gt;&lt;span class=&quot;pre&quot;&gt;get_boolean_mask()&lt;/span&gt;&lt;/code&gt;&lt;/a&gt;&lt;/li&gt;
        &lt;/ul&gt;
        &lt;/li&gt;
        &lt;/ul&gt;
        &lt;/li&gt;
        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/genomic_data.html&quot;&gt;Genomic Data&lt;/a&gt;&lt;ul&gt;
        &lt;li class=&quot;toctree-l2&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/genomic_data.html#api-documentation&quot;&gt;API documentation&lt;/a&gt;&lt;ul&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/genomic_data.html#bionumpy.genomic_data.Genome&quot;&gt;&lt;code class=&quot;docutils literal notranslate&quot;&gt;&lt;span class=&quot;pre&quot;&gt;Genome&lt;/span&gt;&lt;/code&gt;&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/genomic_data.html#bionumpy.genomic_data.GenomicArray&quot;&gt;&lt;code class=&quot;docutils literal notranslate&quot;&gt;&lt;span class=&quot;pre&quot;&gt;GenomicArray&lt;/span&gt;&lt;/code&gt;&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/genomic_data.html#bionumpy.genomic_data.GenomicIntervals&quot;&gt;&lt;code class=&quot;docutils literal notranslate&quot;&gt;&lt;span class=&quot;pre&quot;&gt;GenomicIntervals&lt;/span&gt;&lt;/code&gt;&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/genomic_data.html#bionumpy.genomic_data.GenomicLocation&quot;&gt;&lt;code class=&quot;docutils literal notranslate&quot;&gt;&lt;span class=&quot;pre&quot;&gt;GenomicLocation&lt;/span&gt;&lt;/code&gt;&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/genomic_data.html#bionumpy.genomic_data.GenomicAnnotation&quot;&gt;&lt;code class=&quot;docutils literal notranslate&quot;&gt;&lt;span class=&quot;pre&quot;&gt;GenomicAnnotation&lt;/span&gt;&lt;/code&gt;&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/genomic_data.html#bionumpy.genomic_data.GenomicSequence&quot;&gt;&lt;code class=&quot;docutils literal notranslate&quot;&gt;&lt;span class=&quot;pre&quot;&gt;GenomicSequence&lt;/span&gt;&lt;/code&gt;&lt;/a&gt;&lt;/li&gt;
        &lt;/ul&gt;
        &lt;/li&gt;
        &lt;/ul&gt;
        &lt;/li&gt;
        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/io.html&quot;&gt;IO&lt;/a&gt;&lt;ul&gt;
        &lt;li class=&quot;toctree-l2&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/io.html#api-documentation&quot;&gt;API documentation&lt;/a&gt;&lt;ul&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/io.html#bionumpy.io.bnp_open&quot;&gt;&lt;code class=&quot;docutils literal notranslate&quot;&gt;&lt;span class=&quot;pre&quot;&gt;bnp_open()&lt;/span&gt;&lt;/code&gt;&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/io.html#bionumpy.io.open_indexed&quot;&gt;&lt;code class=&quot;docutils literal notranslate&quot;&gt;&lt;span class=&quot;pre&quot;&gt;open_indexed()&lt;/span&gt;&lt;/code&gt;&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/io.html#bionumpy.io.count_entries&quot;&gt;&lt;code class=&quot;docutils literal notranslate&quot;&gt;&lt;span class=&quot;pre&quot;&gt;count_entries()&lt;/span&gt;&lt;/code&gt;&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/io.html#bionumpy.io.BedBuffer&quot;&gt;&lt;code class=&quot;docutils literal notranslate&quot;&gt;&lt;span class=&quot;pre&quot;&gt;BedBuffer&lt;/span&gt;&lt;/code&gt;&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/io.html#bionumpy.io.VCFBuffer&quot;&gt;&lt;code class=&quot;docutils literal notranslate&quot;&gt;&lt;span class=&quot;pre&quot;&gt;VCFBuffer&lt;/span&gt;&lt;/code&gt;&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/io.html#bionumpy.io.FastQBuffer&quot;&gt;&lt;code class=&quot;docutils literal notranslate&quot;&gt;&lt;span class=&quot;pre&quot;&gt;FastQBuffer&lt;/span&gt;&lt;/code&gt;&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/io.html#bionumpy.io.TwoLineFastaBuffer&quot;&gt;&lt;code class=&quot;docutils literal notranslate&quot;&gt;&lt;span class=&quot;pre&quot;&gt;TwoLineFastaBuffer&lt;/span&gt;&lt;/code&gt;&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/io.html#bionumpy.io.IndexedFasta&quot;&gt;&lt;code class=&quot;docutils literal notranslate&quot;&gt;&lt;span class=&quot;pre&quot;&gt;IndexedFasta&lt;/span&gt;&lt;/code&gt;&lt;/a&gt;&lt;/li&gt;
        &lt;/ul&gt;
        &lt;/li&gt;
        &lt;/ul&gt;
        &lt;/li&gt;
        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/sequences.html&quot;&gt;Sequences&lt;/a&gt;&lt;ul&gt;
        &lt;li class=&quot;toctree-l2&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/sequences.html#api-documentation&quot;&gt;API documentation&lt;/a&gt;&lt;ul&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/sequences.html#bionumpy.sequence.get_kmers&quot;&gt;&lt;code class=&quot;docutils literal notranslate&quot;&gt;&lt;span class=&quot;pre&quot;&gt;get_kmers()&lt;/span&gt;&lt;/code&gt;&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/sequences.html#bionumpy.sequence.get_minimizers&quot;&gt;&lt;code class=&quot;docutils literal notranslate&quot;&gt;&lt;span class=&quot;pre&quot;&gt;get_minimizers()&lt;/span&gt;&lt;/code&gt;&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/sequences.html#bionumpy.sequence.get_motif_scores&quot;&gt;&lt;code class=&quot;docutils literal notranslate&quot;&gt;&lt;span class=&quot;pre&quot;&gt;get_motif_scores()&lt;/span&gt;&lt;/code&gt;&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/sequences.html#bionumpy.sequence.count_encoded&quot;&gt;&lt;code class=&quot;docutils literal notranslate&quot;&gt;&lt;span class=&quot;pre&quot;&gt;count_encoded()&lt;/span&gt;&lt;/code&gt;&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/sequences.html#bionumpy.sequence.match_string&quot;&gt;&lt;code class=&quot;docutils literal notranslate&quot;&gt;&lt;span class=&quot;pre&quot;&gt;match_string()&lt;/span&gt;&lt;/code&gt;&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/sequences.html#bionumpy.sequence.PWM&quot;&gt;&lt;code class=&quot;docutils literal notranslate&quot;&gt;&lt;span class=&quot;pre&quot;&gt;PWM&lt;/span&gt;&lt;/code&gt;&lt;/a&gt;&lt;/li&gt;
        &lt;/ul&gt;
        &lt;/li&gt;
        &lt;/ul&gt;
        &lt;/li&gt;
        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/streams.html&quot;&gt;Streams&lt;/a&gt;&lt;ul&gt;
        &lt;li class=&quot;toctree-l2&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/streams.html#api-documentation&quot;&gt;API documentation&lt;/a&gt;&lt;ul&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/streams.html#bionumpy.streams.streamable&quot;&gt;&lt;code class=&quot;docutils literal notranslate&quot;&gt;&lt;span class=&quot;pre&quot;&gt;streamable()&lt;/span&gt;&lt;/code&gt;&lt;/a&gt;&lt;/li&gt;
        &lt;/ul&gt;
        &lt;/li&gt;
        &lt;/ul&gt;
        &lt;/li&gt;
        &lt;/ul&gt;
        &lt;/div&gt;
        &lt;div class=&quot;toctree-wrapper compound&quot;&gt;
        &lt;p class=&quot;caption&quot; role=&quot;heading&quot;&gt;&lt;span class=&quot;caption-text&quot;&gt;Other&lt;/span&gt;&lt;/p&gt;
        &lt;ul&gt;
        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/developer_guide.html&quot;&gt;Developer guide&lt;/a&gt;&lt;ul&gt;
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        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/sequences.html&quot;&gt;Sequences&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/streams.html&quot;&gt;Streams&lt;/a&gt;&lt;/li&gt;
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        &lt;h1&gt;BioNumPy documentation&lt;a class=&quot;headerlink&quot; href=&quot;https://bionumpy.github.io/bionumpy/menu.html#bionumpy-documentation&quot; title=&quot;Link to this heading&quot;&gt;&lt;/a&gt;&lt;/h1&gt;
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        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/introduction.html&quot;&gt;Getting started with BioNumPy in 10 minutes&lt;/a&gt;&lt;/li&gt;
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        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/tutorials/bam_handling.html&quot;&gt;Working with BAM-files&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/tutorials/subsetting_bed.html&quot;&gt;Getting read pileup inside peaks (intervals)&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/tutorials/fastqc.html&quot;&gt;FastQC-like quality-checking of FASTQ files&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/tutorials/gc_content.html&quot;&gt;Computing GC content inside genes&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/tutorials/position_weight_matrix.html&quot;&gt;Position Weight Matrix&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/tutorials/set_of_sequences.html&quot;&gt;Simulating sequence datasets&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/tutorials/similarity_measures.html&quot;&gt;Computing the similarity between two BED-files&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/tutorials/extracting_kmers_around_snps.html&quot;&gt;Extracting kmers around snps&lt;/a&gt;&lt;/li&gt;
        &lt;/ul&gt;
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        &lt;div class=&quot;toctree-wrapper compound&quot;&gt;
        &lt;p class=&quot;caption&quot; role=&quot;heading&quot;&gt;&lt;span class=&quot;caption-text&quot;&gt;Interoperability&lt;/span&gt;&lt;/p&gt;
        &lt;ul&gt;
        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/interoperability/numpy_operations.html&quot;&gt;Numpy Interoperability&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/interoperability/working_with_biopython.html&quot;&gt;Using BioNumPy with Biopython&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/interoperability/pandas.html&quot;&gt;Pandas Interoperability&lt;/a&gt;&lt;/li&gt;
        &lt;/ul&gt;
        &lt;/div&gt;
        &lt;div class=&quot;toctree-wrapper compound&quot;&gt;
        &lt;p class=&quot;caption&quot; role=&quot;heading&quot;&gt;&lt;span class=&quot;caption-text&quot;&gt;BioNumPy Concepts&lt;/span&gt;&lt;/p&gt;
        &lt;ul&gt;
        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/source/reading_files.html&quot;&gt;Reading files&lt;/a&gt;&lt;ul&gt;
        &lt;li class=&quot;toctree-l2&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/source/reading_files.html#method-1-reading-all-your-data-at-once&quot;&gt;Method 1: Reading all your data at once&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l2&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/source/reading_files.html#method-2-reading-a-single-chunk-from-a-large-file&quot;&gt;Method 2: Reading a single chunk from a large file&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l2&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/source/reading_files.html#method-3-reading-whole-file-as-a-stream-of-chunks&quot;&gt;Method 3: Reading whole file as a stream of chunks&lt;/a&gt;&lt;/li&gt;
        &lt;/ul&gt;
        &lt;/li&gt;
        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/source/encoding.html&quot;&gt;Encodings&lt;/a&gt;&lt;ul&gt;
        &lt;li class=&quot;toctree-l2&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/source/encoding.html#encoding-data-using-a-specific-encoding&quot;&gt;Encoding data using a specific encoding&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l2&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/source/encoding.html#supported-encodings&quot;&gt;Supported encodings&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l2&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/source/encoding.html#when-having-already-encoded-data-advanced-usage&quot;&gt;When having already encoded data (advanced usage)&lt;/a&gt;&lt;/li&gt;
        &lt;/ul&gt;
        &lt;/li&gt;
        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/source/supported_file_formats.html&quot;&gt;Supported file formats&lt;/a&gt;&lt;ul&gt;
        &lt;li class=&quot;toctree-l2&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/source/supported_file_formats.html#example&quot;&gt;Example&lt;/a&gt;&lt;/li&gt;
        &lt;/ul&gt;
        &lt;/li&gt;
        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/source/supported_file_formats.html#reading-a-new-file-format&quot;&gt;Reading a new file format&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/source/sequences.html&quot;&gt;Sequences&lt;/a&gt;&lt;ul&gt;
        &lt;li class=&quot;toctree-l2&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/source/sequences.html#encodedarray&quot;&gt;&lt;cite&gt;EncodedArray&lt;/cite&gt;&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l2&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/source/sequences.html#encodedraggedarray&quot;&gt;&lt;cite&gt;EncodedRaggedArray&lt;/cite&gt;&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l2&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/source/sequences.html#absolute-basics-of-encodedraggedarray&quot;&gt;Absolute basics of &lt;cite&gt;EncodedRaggedArray&lt;/cite&gt;&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l2&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/source/sequences.html#reading-sequences-from-file&quot;&gt;Reading sequences from file&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l2&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/source/sequences.html#functions-workin-on-sequences&quot;&gt;Functions workin on sequences&lt;/a&gt;&lt;/li&gt;
        &lt;/ul&gt;
        &lt;/li&gt;
        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/source/intervals.html&quot;&gt;Intervals&lt;/a&gt;&lt;ul&gt;
        &lt;li class=&quot;toctree-l2&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/source/intervals.html#independent-operations&quot;&gt;Independent Operations&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l2&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/source/intervals.html#operations-with-dependencies&quot;&gt;Operations with dependencies&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l2&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/source/intervals.html#genomic-intervals&quot;&gt;Genomic Intervals&lt;/a&gt;&lt;/li&gt;
        &lt;/ul&gt;
        &lt;/li&gt;
        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/source/multiple_data_sources.html&quot;&gt;Working with Multiple Files/Data Sources&lt;/a&gt;&lt;ul&gt;
        &lt;li class=&quot;toctree-l2&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/source/multiple_data_sources.html#sort-order&quot;&gt;Sort Order&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l2&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/source/multiple_data_sources.html#two-indexed-files&quot;&gt;Two Indexed Files&lt;/a&gt;&lt;/li&gt;
        &lt;/ul&gt;
        &lt;/li&gt;
        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/source/broadcastable_functions.html&quot;&gt;Broadcastable Functions&lt;/a&gt;&lt;ul&gt;
        &lt;li class=&quot;toctree-l2&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/source/broadcastable_functions.html#elementwise-broadcasting-in-numpy&quot;&gt;Elementwise broadcasting in NumPy&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l2&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/source/broadcastable_functions.html#vectorwise-broadcasting&quot;&gt;Vectorwise broadcasting&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l2&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/source/broadcastable_functions.html#sequence-broadcasting&quot;&gt;Sequence broadcasting&lt;/a&gt;&lt;/li&gt;
        &lt;/ul&gt;
        &lt;/li&gt;
        &lt;/ul&gt;
        &lt;/div&gt;
        &lt;div class=&quot;toctree-wrapper compound&quot;&gt;
        &lt;p class=&quot;caption&quot; role=&quot;heading&quot;&gt;&lt;span class=&quot;caption-text&quot;&gt;API documentation&lt;/span&gt;&lt;/p&gt;
        &lt;ul&gt;
        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/bnpdataclass.html&quot;&gt;BnpDataclass&lt;/a&gt;&lt;ul&gt;
        &lt;li class=&quot;toctree-l2&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/bnpdataclass.html#api-documentation&quot;&gt;API documentation&lt;/a&gt;&lt;ul&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/bnpdataclass.html#bionumpy.bnpdataclass.bnpdataclass&quot;&gt;&lt;code class=&quot;docutils literal notranslate&quot;&gt;&lt;span class=&quot;pre&quot;&gt;bnpdataclass()&lt;/span&gt;&lt;/code&gt;&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/bnpdataclass.html#bionumpy.bnpdataclass.replace&quot;&gt;&lt;code class=&quot;docutils literal notranslate&quot;&gt;&lt;span class=&quot;pre&quot;&gt;replace()&lt;/span&gt;&lt;/code&gt;&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/bnpdataclass.html#bionumpy.bnpdataclass.make_dataclass&quot;&gt;&lt;code class=&quot;docutils literal notranslate&quot;&gt;&lt;span class=&quot;pre&quot;&gt;make_dataclass()&lt;/span&gt;&lt;/code&gt;&lt;/a&gt;&lt;/li&gt;
        &lt;/ul&gt;
        &lt;/li&gt;
        &lt;/ul&gt;
        &lt;/li&gt;
        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/genome_arithmetics.html&quot;&gt;Genome arithmetics&lt;/a&gt;&lt;ul&gt;
        &lt;li class=&quot;toctree-l2&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/genome_arithmetics.html#api-documentation&quot;&gt;API documentation&lt;/a&gt;&lt;ul&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/genome_arithmetics.html#bionumpy.arithmetics.forbes&quot;&gt;&lt;code class=&quot;docutils literal notranslate&quot;&gt;&lt;span class=&quot;pre&quot;&gt;forbes()&lt;/span&gt;&lt;/code&gt;&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/genome_arithmetics.html#bionumpy.arithmetics.jaccard&quot;&gt;&lt;code class=&quot;docutils literal notranslate&quot;&gt;&lt;span class=&quot;pre&quot;&gt;jaccard()&lt;/span&gt;&lt;/code&gt;&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/genome_arithmetics.html#bionumpy.arithmetics.sort_intervals&quot;&gt;&lt;code class=&quot;docutils literal notranslate&quot;&gt;&lt;span class=&quot;pre&quot;&gt;sort_intervals()&lt;/span&gt;&lt;/code&gt;&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/genome_arithmetics.html#bionumpy.arithmetics.merge_intervals&quot;&gt;&lt;code class=&quot;docutils literal notranslate&quot;&gt;&lt;span class=&quot;pre&quot;&gt;merge_intervals()&lt;/span&gt;&lt;/code&gt;&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/genome_arithmetics.html#bionumpy.arithmetics.get_pileup&quot;&gt;&lt;code class=&quot;docutils literal notranslate&quot;&gt;&lt;span class=&quot;pre&quot;&gt;get_pileup()&lt;/span&gt;&lt;/code&gt;&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/genome_arithmetics.html#bionumpy.arithmetics.get_boolean_mask&quot;&gt;&lt;code class=&quot;docutils literal notranslate&quot;&gt;&lt;span class=&quot;pre&quot;&gt;get_boolean_mask()&lt;/span&gt;&lt;/code&gt;&lt;/a&gt;&lt;/li&gt;
        &lt;/ul&gt;
        &lt;/li&gt;
        &lt;/ul&gt;
        &lt;/li&gt;
        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/genomic_data.html&quot;&gt;Genomic Data&lt;/a&gt;&lt;ul&gt;
        &lt;li class=&quot;toctree-l2&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/genomic_data.html#api-documentation&quot;&gt;API documentation&lt;/a&gt;&lt;ul&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/genomic_data.html#bionumpy.genomic_data.Genome&quot;&gt;&lt;code class=&quot;docutils literal notranslate&quot;&gt;&lt;span class=&quot;pre&quot;&gt;Genome&lt;/span&gt;&lt;/code&gt;&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/genomic_data.html#bionumpy.genomic_data.GenomicArray&quot;&gt;&lt;code class=&quot;docutils literal notranslate&quot;&gt;&lt;span class=&quot;pre&quot;&gt;GenomicArray&lt;/span&gt;&lt;/code&gt;&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/genomic_data.html#bionumpy.genomic_data.GenomicIntervals&quot;&gt;&lt;code class=&quot;docutils literal notranslate&quot;&gt;&lt;span class=&quot;pre&quot;&gt;GenomicIntervals&lt;/span&gt;&lt;/code&gt;&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/genomic_data.html#bionumpy.genomic_data.GenomicLocation&quot;&gt;&lt;code class=&quot;docutils literal notranslate&quot;&gt;&lt;span class=&quot;pre&quot;&gt;GenomicLocation&lt;/span&gt;&lt;/code&gt;&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/genomic_data.html#bionumpy.genomic_data.GenomicAnnotation&quot;&gt;&lt;code class=&quot;docutils literal notranslate&quot;&gt;&lt;span class=&quot;pre&quot;&gt;GenomicAnnotation&lt;/span&gt;&lt;/code&gt;&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/genomic_data.html#bionumpy.genomic_data.GenomicSequence&quot;&gt;&lt;code class=&quot;docutils literal notranslate&quot;&gt;&lt;span class=&quot;pre&quot;&gt;GenomicSequence&lt;/span&gt;&lt;/code&gt;&lt;/a&gt;&lt;/li&gt;
        &lt;/ul&gt;
        &lt;/li&gt;
        &lt;/ul&gt;
        &lt;/li&gt;
        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/io.html&quot;&gt;IO&lt;/a&gt;&lt;ul&gt;
        &lt;li class=&quot;toctree-l2&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/io.html#api-documentation&quot;&gt;API documentation&lt;/a&gt;&lt;ul&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/io.html#bionumpy.io.bnp_open&quot;&gt;&lt;code class=&quot;docutils literal notranslate&quot;&gt;&lt;span class=&quot;pre&quot;&gt;bnp_open()&lt;/span&gt;&lt;/code&gt;&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/io.html#bionumpy.io.open_indexed&quot;&gt;&lt;code class=&quot;docutils literal notranslate&quot;&gt;&lt;span class=&quot;pre&quot;&gt;open_indexed()&lt;/span&gt;&lt;/code&gt;&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/io.html#bionumpy.io.count_entries&quot;&gt;&lt;code class=&quot;docutils literal notranslate&quot;&gt;&lt;span class=&quot;pre&quot;&gt;count_entries()&lt;/span&gt;&lt;/code&gt;&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/io.html#bionumpy.io.BedBuffer&quot;&gt;&lt;code class=&quot;docutils literal notranslate&quot;&gt;&lt;span class=&quot;pre&quot;&gt;BedBuffer&lt;/span&gt;&lt;/code&gt;&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/io.html#bionumpy.io.VCFBuffer&quot;&gt;&lt;code class=&quot;docutils literal notranslate&quot;&gt;&lt;span class=&quot;pre&quot;&gt;VCFBuffer&lt;/span&gt;&lt;/code&gt;&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/io.html#bionumpy.io.FastQBuffer&quot;&gt;&lt;code class=&quot;docutils literal notranslate&quot;&gt;&lt;span class=&quot;pre&quot;&gt;FastQBuffer&lt;/span&gt;&lt;/code&gt;&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/io.html#bionumpy.io.TwoLineFastaBuffer&quot;&gt;&lt;code class=&quot;docutils literal notranslate&quot;&gt;&lt;span class=&quot;pre&quot;&gt;TwoLineFastaBuffer&lt;/span&gt;&lt;/code&gt;&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/io.html#bionumpy.io.IndexedFasta&quot;&gt;&lt;code class=&quot;docutils literal notranslate&quot;&gt;&lt;span class=&quot;pre&quot;&gt;IndexedFasta&lt;/span&gt;&lt;/code&gt;&lt;/a&gt;&lt;/li&gt;
        &lt;/ul&gt;
        &lt;/li&gt;
        &lt;/ul&gt;
        &lt;/li&gt;
        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/sequences.html&quot;&gt;Sequences&lt;/a&gt;&lt;ul&gt;
        &lt;li class=&quot;toctree-l2&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/sequences.html#api-documentation&quot;&gt;API documentation&lt;/a&gt;&lt;ul&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/sequences.html#bionumpy.sequence.get_kmers&quot;&gt;&lt;code class=&quot;docutils literal notranslate&quot;&gt;&lt;span class=&quot;pre&quot;&gt;get_kmers()&lt;/span&gt;&lt;/code&gt;&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/sequences.html#bionumpy.sequence.get_minimizers&quot;&gt;&lt;code class=&quot;docutils literal notranslate&quot;&gt;&lt;span class=&quot;pre&quot;&gt;get_minimizers()&lt;/span&gt;&lt;/code&gt;&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/sequences.html#bionumpy.sequence.get_motif_scores&quot;&gt;&lt;code class=&quot;docutils literal notranslate&quot;&gt;&lt;span class=&quot;pre&quot;&gt;get_motif_scores()&lt;/span&gt;&lt;/code&gt;&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/sequences.html#bionumpy.sequence.count_encoded&quot;&gt;&lt;code class=&quot;docutils literal notranslate&quot;&gt;&lt;span class=&quot;pre&quot;&gt;count_encoded()&lt;/span&gt;&lt;/code&gt;&lt;/a&gt;&lt;/li&gt;
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        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/modules/streams.html&quot;&gt;Streams&lt;/a&gt;&lt;ul&gt;
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        &lt;div class=&quot;toctree-wrapper compound&quot;&gt;
        &lt;p class=&quot;caption&quot; role=&quot;heading&quot;&gt;&lt;span class=&quot;caption-text&quot;&gt;Other&lt;/span&gt;&lt;/p&gt;
        &lt;ul&gt;
        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/developer_guide.html&quot;&gt;Developer guide&lt;/a&gt;&lt;ul&gt;
        &lt;li class=&quot;toctree-l2&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/developer_guide/getting_started.html&quot;&gt;Getting started and how to contribute&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l2&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/developer_guide/setting_up_development_environment.html&quot;&gt;Setting up your development environment&lt;/a&gt;&lt;ul&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/developer_guide/setting_up_development_environment.html#step-1-optional-install-development-version-of-npstructures&quot;&gt;Step 1 (Optional): Install development version of npstructures&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/developer_guide/setting_up_development_environment.html#step-2-install-bionumpy-locally-not-from-pypi&quot;&gt;Step 2: Install BioNumPy locally (not from PyPi)&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/developer_guide/setting_up_development_environment.html#step-3-install-development-dependencies&quot;&gt;Step 3: Install development dependencies&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/developer_guide/setting_up_development_environment.html#step-4-test-your-installation&quot;&gt;Step 4: Test your installation&lt;/a&gt;&lt;/li&gt;
        &lt;/ul&gt;
        &lt;/li&gt;
        &lt;li class=&quot;toctree-l2&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/developer_guide/testing.html&quot;&gt;How we do testing in BioNumPy&lt;/a&gt;&lt;ul&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/developer_guide/testing.html#dependencies-with-npstructures&quot;&gt;Dependencies with NpStructures&lt;/a&gt;&lt;/li&gt;
        &lt;/ul&gt;
        &lt;/li&gt;
        &lt;li class=&quot;toctree-l2&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/developer_guide/making_examples.html&quot;&gt;Making examples&lt;/a&gt;&lt;ul&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/developer_guide/making_examples.html#overview&quot;&gt;Overview&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/developer_guide/making_examples.html#testing-of-examples&quot;&gt;Testing of examples&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/developer_guide/making_examples.html#using-data-in-your-examples&quot;&gt;Using data in your examples&lt;/a&gt;&lt;/li&gt;
        &lt;/ul&gt;
        &lt;/li&gt;
        &lt;li class=&quot;toctree-l2&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/developer_guide/writing_documentation.html&quot;&gt;Writing documentation&lt;/a&gt;&lt;ul&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/developer_guide/writing_documentation.html#structure-of-documentation&quot;&gt;Structure of documentation&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/developer_guide/writing_documentation.html#writing-code-in-the-documentation&quot;&gt;Writing code in the documentation&lt;/a&gt;&lt;/li&gt;
        &lt;/ul&gt;
        &lt;/li&gt;
        &lt;li class=&quot;toctree-l2&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/developer_guide/design_principles.html&quot;&gt;Design principles and code overview&lt;/a&gt;&lt;ul&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/developer_guide/design_principles.html#overview&quot;&gt;Overview&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/developer_guide/design_principles.html#vectorized-file-i-o&quot;&gt;Vectorized File I/O&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/developer_guide/design_principles.html#bnpdataclass&quot;&gt;&lt;cite&gt;@bnpdataclass&lt;/cite&gt;&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/developer_guide/design_principles.html#utility-functions&quot;&gt;Utility Functions&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/developer_guide/design_principles.html#encodings&quot;&gt;Encodings&lt;/a&gt;&lt;/li&gt;
        &lt;/ul&gt;
        &lt;/li&gt;
        &lt;li class=&quot;toctree-l2&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/developer_guide/encodings.html&quot;&gt;Implementing encodings&lt;/a&gt;&lt;/li&gt;
        &lt;/ul&gt;
        &lt;/li&gt;
        &lt;li class=&quot;toctree-l1&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/manuscript/index.html&quot;&gt;BioNumPy manuscript&lt;/a&gt;&lt;ul&gt;
        &lt;li class=&quot;toctree-l2&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/manuscript/index.html#abstract&quot;&gt;Abstract&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l2&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/manuscript/index.html#introduction&quot;&gt;Introduction&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l2&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/manuscript/index.html#results&quot;&gt;Results&lt;/a&gt;&lt;ul&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/manuscript/index.html#the-bionumpy-library&quot;&gt;The BioNumPy Library&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/manuscript/index.html#benchmarks&quot;&gt;Benchmarks&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/manuscript/index.html#example-usage&quot;&gt;Example usage&lt;/a&gt;&lt;ul&gt;
        &lt;li class=&quot;toctree-l4&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/manuscript/index.html#example-1-using-bionumpy-on-sequence-data&quot;&gt;Example 1: Using BioNumPy on sequence data&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l4&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/manuscript/index.html#example-2-analysing-motif-matches-inside-transcription-factor-peaks&quot;&gt;Example 2: Analysing motif matches inside transcription factor peaks&lt;/a&gt;&lt;/li&gt;
        &lt;/ul&gt;
        &lt;/li&gt;
        &lt;/ul&gt;
        &lt;/li&gt;
        &lt;li class=&quot;toctree-l2&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/manuscript/index.html#implementation-details&quot;&gt;Implementation details&lt;/a&gt;&lt;ul&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/manuscript/index.html#data-representation&quot;&gt;Data representation&lt;/a&gt;&lt;/li&gt;
        &lt;li class=&quot;toctree-l3&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/manuscript/index.html#development&quot;&gt;Development&lt;/a&gt;&lt;/li&gt;
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        &lt;li class=&quot;toctree-l2&quot;&gt;&lt;a class=&quot;reference internal&quot; href=&quot;https://bionumpy.github.io/bionumpy/manuscript/index.html#discussion&quot;&gt;Discussion&lt;/a&gt;&lt;/li&gt;
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@TonyRL TonyRL merged commit 9916c34 into DIYgod:master Oct 26, 2024
54 of 55 checks passed
@x1e5c x1e5c deleted the patch-1 branch November 10, 2024 10:25
artefaritaKuniklo pushed a commit to artefaritaKuniklo/RSSHub that referenced this pull request Dec 13, 2024
@x1e5c @artefaritaKuniklo
fix(route): get correct item link (DIYgod#17278)
c5fb7c0 
When the `href` link inside the element is a relative link, the original handling would obtain an incorrect full link
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@x1e5c @TonyRL