Merge pull request #202 from jeromekelleher/move-cli-reference

Move cli reference

Author: jeromekelleher

docs/_toc.yml

@@ -2,6 +2,10 @@ format: jb-book
 root: intro
 chapters:
 - file: installation
-- file: vcf2zarr
-- file: vcfpartition
-- file: cli
+- file: vcf2zarr/overview
+  sections:
+  - file: vcf2zarr/tutorial
+  - file: vcf2zarr/cli_ref
+- file: vcfpartition/overview
+  sections:
+  - file: vcfpartition/cli_ref

docs/cli.md renamed to docs/vcf2zarr/cli_ref.md

@@ -8,6 +8,7 @@
 % Based on: https://github.com/skypilot-org/skypilot/pull/2834
 
 ```{eval-rst}
+
 .. _cmd-vcf2zarr:
 .. click:: bio2zarr.cli:vcf2zarr_main
    :prog: vcf2zarr
@@ -32,6 +33,7 @@
 ## Explode
 
 ```{eval-rst}
+.. _cmd-vcf2zarr-explode:
 .. click:: bio2zarr.cli:explode
    :prog: vcf2zarr explode
    :nested: full

docs/vcf2zarr.md renamed to docs/vcf2zarr/overview.md

@@ -1,20 +1,6 @@
----
-jupytext:
-  formats: md:myst
-  text_representation:
-    extension: .md
-    format_name: myst
-kernelspec:
-  display_name: Bash
-  language: bash
-  name: bash
----
 # vcf2zarr
 
 
-## Overview
-
-
 Convert a VCF to zarr format:
 
 ```
@@ -99,31 +85,3 @@ to encode allows you to try out these options on small subsets, hopefully
 arriving at settings with the desired balance of compression and query
 performance.
 
-
-
-## Tutorial
-
-This is a step-by-step tutorial showing you how to convert your
-VCF data into Zarr format. There's three different ways to
-convert your data, basically providing different levels of
-convenience and flexibility corresponding to what you might
-need for small, intermediate and large datasets.
-
-### Small
-
-<!-- ```{code-cell} bash -->
-<!-- vcf2zarr convert ../tests/data/vcf/sample.vcf.gz sample.zarr -vf -->
-<!-- ``` -->
-
- <div id="vcf2zarr_convert"></div>
- <script>
- AsciinemaPlayer.create('_static/vcf2zarr_convert.cast',
-    document.getElementById('vcf2zarr_convert'), {
-    cols:80,
-    rows:12
- });
- </script>
-
-### Intermediate
-
-### Large

docs/vcf2zarr/tutorial.md

@@ -0,0 +1,38 @@
+---
+jupytext:
+  formats: md:myst
+  text_representation:
+    extension: .md
+    format_name: myst
+kernelspec:
+  display_name: Bash
+  language: bash
+  name: bash
+---
+# Tutorial
+
+This is a step-by-step tutorial showing you how to convert your
+VCF data into Zarr format. There's three different ways to
+convert your data, basically providing different levels of
+convenience and flexibility corresponding to what you might
+need for small, intermediate and large datasets.
+
+## Small
+
+<!-- ```{code-cell} bash -->
+<!-- vcf2zarr convert ../tests/data/vcf/sample.vcf.gz sample.zarr -vf -->
+<!-- ``` -->
+
+ <div id="vcf2zarr_convert"></div>
+ <script>
+ AsciinemaPlayer.create('_static/vcf2zarr_convert.cast',
+    document.getElementById('vcf2zarr_convert'), {
+    cols:80,
+    rows:12
+ });
+ </script>
+
+## Intermediate
+
+## Large
+

docs/vcfpartition/cli_ref.md

@@ -0,0 +1,8 @@
+# CLI Reference
+
+
+```{eval-rst}
+.. click:: bio2zarr.cli:vcfpartition
+   :prog: vcfpartition
+   :nested: full
+```

docs/vcfpartition.md renamed to docs/vcfpartition/overview.md

@@ -26,5 +26,4 @@ into chunks for parallelisation.
 
 **TODO give a nice example here using xargs**
 
-**WARNING that this does not take into account that indels may overlap
-partitions and you may count variants twice or more if they do**
+**WARNING that this does not take into account that indels may overlap**