From f9df6abacb4eb2c06b59e6b6e6466139ba06e17d Mon Sep 17 00:00:00 2001
From: Alison Meynert <alison@fulcrumgenomics.com>
Date: Fri, 10 Apr 2026 13:58:29 -0700
Subject: [PATCH 1/4] feat: register all new tools in main.py

Register compute_haplotype_statistics, compute_haplotypes,
compute_variation_ratios, create_fasta_and_index, create_gnomad_sites_vcf,
extract_gnomad_afs, remap_divref, and rewrite_fasta in the defopt tool
list. All 18 parametrized tests pass.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 divref/divref/main.py | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/divref/divref/main.py b/divref/divref/main.py
index 0e7127b..8ac18a5 100644
--- a/divref/divref/main.py
+++ b/divref/divref/main.py
@@ -5,10 +5,26 @@
 
 import defopt
 
+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.hello import hello
+from divref.tools.remap_divref import remap_divref
+from divref.tools.rewrite_fasta import rewrite_fasta
 
 _tools: List[Callable[..., None]] = [
+    compute_haplotype_statistics,
+    compute_haplotypes,
+    compute_variation_ratios,
+    create_fasta_and_index,
+    create_gnomad_sites_vcf,
+    extract_gnomad_afs,
     hello,
+    remap_divref,
+    rewrite_fasta,
 ]
 
 

From c947dd2d6d716c90b61e34749f86b458587e2fa4 Mon Sep 17 00:00:00 2001
From: Alison Meynert <alison@fulcrumgenomics.com>
Date: Fri, 10 Apr 2026 14:13:05 -0700
Subject: [PATCH 2/4] chore: remove hello.py tool

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 divref/divref/main.py        |  2 --
 divref/divref/tools/hello.py | 11 -----------
 2 files changed, 13 deletions(-)
 delete mode 100644 divref/divref/tools/hello.py

diff --git a/divref/divref/main.py b/divref/divref/main.py
index 8ac18a5..f7f9979 100644
--- a/divref/divref/main.py
+++ b/divref/divref/main.py
@@ -11,7 +11,6 @@
 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.hello import hello
 from divref.tools.remap_divref import remap_divref
 from divref.tools.rewrite_fasta import rewrite_fasta
 
@@ -22,7 +21,6 @@
     create_fasta_and_index,
     create_gnomad_sites_vcf,
     extract_gnomad_afs,
-    hello,
     remap_divref,
     rewrite_fasta,
 ]
diff --git a/divref/divref/tools/hello.py b/divref/divref/tools/hello.py
deleted file mode 100644
index 775129f..0000000
--- a/divref/divref/tools/hello.py
+++ /dev/null
@@ -1,11 +0,0 @@
-def hello(
-    *,
-    name: str = "World",
-) -> None:
-    """
-    Print a greeting.
-
-    Args:
-        name: The person to greet.
-    """
-    print(f"Hello, {name}!")

From 66f71b2d3a245df7b0b0d38cc26d1709dc6d5794 Mon Sep 17 00:00:00 2001
From: Alison Meynert <alison@fulcrumgenomics.com>
Date: Fri, 10 Apr 2026 14:13:32 -0700
Subject: [PATCH 3/4] chore: update .gitignore

---
 .gitignore | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.gitignore b/.gitignore
index 0e5e367..2943aae 100644
--- a/.gitignore
+++ b/.gitignore
@@ -21,4 +21,4 @@
 !.pixi/config.toml
 
 # claude
-**/claude
+**/.claude

From 0f92c31cd8853ee33c3cdb735d1250c5e78e282f Mon Sep 17 00:00:00 2001
From: Alison Meynert <alison@fulcrumgenomics.com>
Date: Fri, 10 Apr 2026 14:13:43 -0700
Subject: [PATCH 4/4] feat: update README with description

---
 README.md | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/README.md b/README.md
index 31a1b86..e89110e 100644
--- a/README.md
+++ b/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`.