Merge pull request #4 from jeromekelleher/readme-update

Initial README

Author: jeromekelleher

README.md

@@ -1,4 +1,53 @@
 # bio2zarr
 Convert bioinformatics file formats to Zarr
 
-**This is early alpha-status code: DO NOT USE!!**
+Initially supports converting VCF to the
+[sgkit vcf-zarr specification](https://github.com/pystatgen/vcf-zarr-spec/)
+
+**This is early alpha-status code: everything is subject to change, a
+and it has not been thoroughly tested**
+
+## Usage
+
+Convert a VCF to zarr format:
+
+```
+python3 -m bio2zarr vcf2zarr convert <VCF> <zarr>
+```
+
+Converts the VCF to zarr format.
+
+**Do not use this for anything but the smallest files**
+
+The recommended approach is to use a multi-stage conversion
+
+First, convert the VCF into an intermediate columnar format:
+
+```
+python3 -m bio2zarr vcf2zarr convert tests/data/vcf/sample.vcf.gz tmp/sample.exploded
+```
+
+Then, (optionally) inspect this representation to get a feel for your dataset
+```
+python3 -m bio2zarr vcf2zarr summarise tmp/sample.exploded
+```
+
+Then, (optionally) generate a conversion schema to describe the corresponding
+Zarr arrays:
+
+```
+python3 -m bio2zarr vcf2zarr genspec tmp/sample.exploded > sample.schema.json
+```
+
+View and edit the schema, deleting any columns you don't want.
+
+Finally, convert to Zarr
+
+```
+python3 -m bio2zarr vcf2zarr to-zarr tmp/sample.exploded tmp/sample.zarr -s sample.schema.json
+```
+
+Use the ``-p, --worker-processes`` argument to control the number of workers used
+to do zarr encoding.
+
+