From d7f44b031614cececa35dd9a99c5feeb64b4c7a7 Mon Sep 17 00:00:00 2001
From: Will Rowe <w.p.m.rowe@gmail.com>
Date: Tue, 15 Sep 2026 16:47:11 +0100
Subject: [PATCH 1/2] fix: add github actions ci and main links

---
 .github/workflows/ci.yml | 32 ++++++++++++++++++++++++++++++++
 README.md                |  4 ++--
 cmd/get.go               |  2 +-
 docs/tutorial.md         |  2 +-
 4 files changed, 36 insertions(+), 4 deletions(-)
 create mode 100644 .github/workflows/ci.yml

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
new file mode 100644
index 0000000..0fdeb23
--- /dev/null
+++ b/.github/workflows/ci.yml
@@ -0,0 +1,32 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - master
+      - main
+      - bug-fixes
+  pull_request:
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Set up Go
+        uses: actions/setup-go@v5
+        with:
+          go-version: '1.27'
+          cache: true
+
+      - name: Download dependencies
+        run: go get -d -t -v ./...
+
+      - name: Run tests
+        run: go test -v ./...
+
+      - name: Build
+        run: go build -v ./...
diff --git a/README.md b/README.md
index a6b26b9..9f5fdea 100644
--- a/README.md
+++ b/README.md
@@ -4,10 +4,10 @@
   <img src="misc/groot-logo-with-text.png?raw=true?" alt="groot-logo" width="250">
   <h3><a style="color:#D5672C">G</a>raphing <a style="color:#D5672C">R</a>esistance <a style="color:#D5672C">O</a>ut <a style="color:#D5672C">O</a>f me<a style="color:#D5672C">T</a>agenomes</h3>
   <hr>
-  <a href="https://gitlab.com/will-rowe/groot/-/pipelines"><img src="https://img.shields.io/badge/ci-gitlab-orange.svg" alt="gitlab-ci"></a>
+  <a href="https://github.com/will-rowe/groot/actions/workflows/ci.yml"><img src="https://img.shields.io/badge/ci-github%20actions-blue.svg" alt="github-actions"></a>
   <a href='http://groot-documentation.readthedocs.io/en/latest/?badge=latest'><img src='https://readthedocs.org/projects/groot-documentation/badge/?version=latest' alt='Documentation Status' /></a>
   <a href="https://goreportcard.com/report/github.com/will-rowe/groot"><img src="https://goreportcard.com/badge/github.com/will-rowe/groot" alt="reportcard"></a>
-  <a href="https://github.com/will-rowe/groot/blob/master/LICENSE"><img src="https://img.shields.io/badge/license-MIT-orange.svg" alt="License"></a>
+  <a href="https://github.com/will-rowe/groot/blob/main/LICENSE"><img src="https://img.shields.io/badge/license-MIT-orange.svg" alt="License"></a>
   <a href="https://zenodo.org/badge/latestdoi/117543539"><img src="https://zenodo.org/badge/117543539.svg" alt="DOI"></a>
   <a href="https://gitter.im/groot-help/Lobby"><img src="https://img.shields.io/badge/chat-gitter-8A2BE2.svg" alt="gitter"></a>
   <a href="https://bioconda.github.io/recipes/groot/README.html"><img src="https://anaconda.org/bioconda/groot/badges/downloads.svg" alt="bioconda"></a>
diff --git a/cmd/get.go b/cmd/get.go
index b5ed620..ea9075e 100644
--- a/cmd/get.go
+++ b/cmd/get.go
@@ -46,7 +46,7 @@ var md5sums = map[string]string{
 }
 
 // dbUrl to download databases from
-var dbURL = fmt.Sprintf("https://github.com/will-rowe/groot/raw/master/db/clustered-ARG-databases/%v/", version.GetBaseVersion())
+var dbURL = fmt.Sprintf("https://github.com/will-rowe/groot/raw/main/db/clustered-ARG-databases/%v/", version.GetBaseVersion())
 
 // the command line arguments
 var (
diff --git a/docs/tutorial.md b/docs/tutorial.md
index 135a314..39666bf 100644
--- a/docs/tutorial.md
+++ b/docs/tutorial.md
@@ -284,7 +284,7 @@ Now we have a set of ARGs we know are present in one or more samples, we might w
 Download the full ARG-ANNOT set of genes and then index with samtools:
 
 ```bash
-wget https://github.com/will-rowe/groot/raw/master/db/full-ARG-databases/arg-annot-db/argannot-args.fna
+wget https://github.com/will-rowe/groot/raw/main/db/full-ARG-databases/arg-annot-db/argannot-args.fna
 samtools faidx argannot-args.fna
 ```
 

From e17b22f4230ea519db37e5c93c661f8408ac36dc Mon Sep 17 00:00:00 2001
From: Will Rowe <w.p.m.rowe@gmail.com>
Date: Tue, 15 Sep 2026 14:27:33 +0100
Subject: [PATCH 2/2] Update addWindow function to track maxSpan

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
---
 src/graph/graph.go | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/src/graph/graph.go b/src/graph/graph.go
index 4c22e69..3b2e8c1 100644
--- a/src/graph/graph.go
+++ b/src/graph/graph.go
@@ -252,7 +252,10 @@ func (GrootGraph *GrootGraph) WindowGraph(windowSize, kmerSize, sketchSize int)
 	}
 
 	windowLookup := make(map[windowLocation]lshe.Keys)
-	addWindow := func(window lshe.Key) {
+addWindow := func(window lshe.Key) {
+		if window.MergeSpan > GrootGraph.maxSpan {
+			GrootGraph.maxSpan = window.MergeSpan
+		}
 		key := windowLocation{graphID: window.GraphID, node: window.Node, offset: window.OffSet}
 
 		if existingWindowLocation, ok := windowLookup[key]; ok {