Partial rearrangement

Author: jeromekelleher

docs/_toc.yml

@@ -4,4 +4,3 @@ chapters:
 - file: installation
 - file: vcf2zarr
 - file: vcfpartition
-- file: cli

docs/cli.md

@@ -9,6 +9,7 @@ kernelspec:
   language: bash
   name: bash
 ---
+(sec_vcf2zarr)=
 # vcf2zarr
 
 
@@ -127,3 +128,83 @@ need for small, intermediate and large datasets.
 ### Intermediate
 
 ### Large
+
+## CLI Reference
+
+% A note on cross references... There's some weird long-standing problem with
+% cross referencing program values in Sphinx, which means that we can't use
+% the built-in labels generated by sphinx-click. We can make our own explicit
+% targets, but these have to have slightly weird names to avoid conflicting
+% with what sphinx-click is doing. So, hence the cmd- prefix.
+% Based on: https://github.com/skypilot-org/skypilot/pull/2834
+
+<!-- .. _cmd-vcf2zarr: -->
+<!-- .. click:: bio2zarr.cli:vcf2zarr_main -->
+<!--    :prog: vcf2zarr -->
+<!--    :nested: short -->
+
+```{eval-rst}
+
+.. _cmd-vcf2zarr-convert:
+.. click:: bio2zarr.cli:convert_vcf
+   :prog: vcf2zarr convert
+   :nested: full
+
+.. _cmd-vcf2zarr-inspect:
+.. click:: bio2zarr.cli:inspect
+   :prog: vcf2zarr inspect
+   :nested: full
+
+.. _cmd-vcf2zarr-mkschema:
+.. click:: bio2zarr.cli:mkschema
+   :prog: vcf2zarr mkschema
+   :nested: full
+```
+
+### Explode
+
+```{eval-rst}
+.. _cmd-vcf2zarr-explode:
+.. click:: bio2zarr.cli:explode
+   :prog: vcf2zarr explode
+   :nested: full
+
+.. _cmd-vcf2zarr-dexplode-init:
+.. click:: bio2zarr.cli:dexplode_init
+   :prog: vcf2zarr dexplode-init
+   :nested: full
+
+.. _cmd-vcf2zarr-dexplode-partition:
+.. click:: bio2zarr.cli:dexplode_partition
+   :prog: vcf2zarr dexplode-partition
+   :nested: full
+
+.. _cmd-vcf2zarr-dexplode-finalise:
+.. click:: bio2zarr.cli:dexplode_finalise
+   :prog: vcf2zarr dexplode-finalise
+   :nested: full
+```
+
+### Encode
+
+```{eval-rst}
+.. click:: bio2zarr.cli:encode
+   :prog: vcf2zarr encode
+   :nested: full
+
+.. _cmd-vcf2zarr-dencode-init:
+.. click:: bio2zarr.cli:dencode_init
+   :prog: vcf2zarr dencode-init
+   :nested: full
+
+.. _cmd-vcf2zarr-dencode-partition:
+.. click:: bio2zarr.cli:dencode_partition
+   :prog: vcf2zarr dencode-partition
+   :nested: full
+
+.. _cmd-vcf2zarr-dencode-finalise:
+.. click:: bio2zarr.cli:dencode_finalise
+   :prog: vcf2zarr dencode-finalise
+   :nested: full
+```
+

docs/vcf2zarr.md

@@ -1,4 +1,5 @@
-# vcfpartition
+(xxx_vcfpartition)=
+# vcfpartition xxx
 
 ## Overview
 
@@ -26,5 +27,15 @@ 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**
+
+
+## CLI Reference
+
+FIXME not working due to
+
+```{eval-rst}
+.. click:: bio2zarr.cli:vcfpartition
+   :prog: vcfpartition
+   :nested: full
+```