feat: register tools, remove hello.py, update README

.gitignore

@@ -21,4 +21,4 @@
 !.pixi/config.toml
 
 # claude
-**/claude
+**/.claude

README.md

@@ -7,6 +7,13 @@
 
 # Snakemake workflow implementation to create DivRef-style resource
 
+This workflow is inspired by the [DivRef](https://github.com/e9genomics/human-diversity-reference) repository which is used to generate a bundle of FASTA sequences and a corresponding DuckDB index of common human variation.
+
+The original implementation is via a set of standalone Python scripts and a Makefile.
+This implementation:
+1. Wraps the Python scripts in a toolkit with added typing, improved parameterization, and added unit testing.
+2. Adds a Snakemake workflow and associated configuration to drive the resource generation process.
+
 ## Set up Environment
 
 The environment for this analysis is managed using `pixi`.

divref/divref/main.py

@@ -5,10 +5,24 @@
 
 import defopt
 
-from divref.tools.hello import hello
+from divref.tools.compute_haplotype_statistics import compute_haplotype_statistics
+from divref.tools.compute_haplotypes import compute_haplotypes
+from divref.tools.compute_variation_ratios import compute_variation_ratios
+from divref.tools.create_fasta_and_index import create_fasta_and_index
+from divref.tools.create_gnomad_sites_vcf import create_gnomad_sites_vcf
+from divref.tools.extract_gnomad_afs import extract_gnomad_afs
+from divref.tools.remap_divref import remap_divref
+from divref.tools.rewrite_fasta import rewrite_fasta
 
 _tools: List[Callable[..., None]] = [
-    hello,
+    compute_haplotype_statistics,
+    compute_haplotypes,
+    compute_variation_ratios,
+    create_fasta_and_index,
+    create_gnomad_sites_vcf,
+    extract_gnomad_afs,
+    remap_divref,
+    rewrite_fasta,
 ]