From 71fe7dff4b14a50b01b4580abda3131d52f3768f Mon Sep 17 00:00:00 2001
From: Adityarup Laha <me@adityaruplaha.me>
Date: Sat, 27 Dec 2025 14:09:51 +0530
Subject: [PATCH 1/4] Add plink1.9 to Packages.

---
 BioArchLinux/plink1.9/PKGBUILD   | 42 ++++++++++++++++++++++++++++++++
 BioArchLinux/plink1.9/lilac.yaml | 11 +++++++++
 2 files changed, 53 insertions(+)
 create mode 100644 BioArchLinux/plink1.9/PKGBUILD
 create mode 100644 BioArchLinux/plink1.9/lilac.yaml

diff --git a/BioArchLinux/plink1.9/PKGBUILD b/BioArchLinux/plink1.9/PKGBUILD
new file mode 100644
index 0000000000..58a614fa77
--- /dev/null
+++ b/BioArchLinux/plink1.9/PKGBUILD
@@ -0,0 +1,42 @@
+# Maintainer: Adityarup Laha <me@adityaruplaha.me>
+# Maintainer: Chris Vittal <chris@vittal.dev>
+_pkgname='plink1.9'
+pkgname="$_pkgname-git"
+# Upstream has changed tag formats, epoch is necessary
+epoch=1
+_pkgver=1.9
+pkgver=1.9.b.7.11.r64.gacb45ef4
+pkgrel=1
+pkgdesc="whole-genome association analysis toolset, version 1.9"
+arch=(x86_64)
+license=(GPL-3.0-only)
+url="https://www.cog-genomics.org/plink/1.9/"
+source=('plink1.9::git+https://github.com/chrchang/plink-ng.git'
+        'bin-name.patch')
+depends=('zlib>=1.2.4' 'cblas' 'lapack')
+makedepends=('git')
+provides=('plink1.9')
+sha256sums=(SKIP
+            24f570e751f51b6ab05c29f92cad4a57b0a54b7bb4a81dd067cf1cdc1c887327)
+
+prepare() {
+    cd "$_pkgname/$_pkgver"
+    patch -i "${srcdir}/bin-name.patch"
+}
+
+build() {
+    cd "$_pkgname/$_pkgver"
+    CFLAGS+=" -DDYNAMIC_ZLIB $(pkg-config --cflags lapack blas cblas)" CXXFLAGS+=' -DDYNAMIC_ZLIB'\
+        BLASFLAGS=$(pkg-config --libs lapack blas cblas) ZLIB=-lz \
+        LDFLAGS+=' -lpthread -lm' BIN=$_pkgname make -f Makefile
+}
+
+package() {
+    cd "$_pkgname/$_pkgver"
+    BIN="$_pkgname" DESTDIR="$pkgdir" PREFIX=/usr make -f Makefile install
+}
+
+pkgver() {
+    cd "$_pkgname"
+    echo "$_pkgver"."$(git describe --tags --long --match "v1.9*" | sed -E 's/^[^-]+-([^-]+)-([0-9]+)-(g[a-f0-9]+)/\1.r\2.\3/')"
+}
diff --git a/BioArchLinux/plink1.9/lilac.yaml b/BioArchLinux/plink1.9/lilac.yaml
new file mode 100644
index 0000000000..c4375e2f31
--- /dev/null
+++ b/BioArchLinux/plink1.9/lilac.yaml
@@ -0,0 +1,11 @@
+build_prefix: extra-x86_64
+maintainers:
+  - github: adityaruplaha
+    email: me@adityaruplaha.me
+post_build_script: |
+  git_pkgbuild_commit()
+update_on:
+  - source: github
+    github: chrchang/plink-ng
+    use_latest_release: true
+    prefix: 'v'

From 3f17cbd373602c0ba499fe5cc6adf115f317789a Mon Sep 17 00:00:00 2001
From: Adityarup Laha <me@adityaruplaha.me>
Date: Sat, 27 Dec 2025 14:22:37 +0530
Subject: [PATCH 2/4] Add missing patch and resolve Copilot review comments.

---
 BioArchLinux/plink1.9/PKGBUILD       |  6 +-----
 BioArchLinux/plink1.9/bin-name.patch | 16 ++++++++++++++++
 2 files changed, 17 insertions(+), 5 deletions(-)
 create mode 100644 BioArchLinux/plink1.9/bin-name.patch

diff --git a/BioArchLinux/plink1.9/PKGBUILD b/BioArchLinux/plink1.9/PKGBUILD
index 58a614fa77..0c5c507881 100644
--- a/BioArchLinux/plink1.9/PKGBUILD
+++ b/BioArchLinux/plink1.9/PKGBUILD
@@ -1,9 +1,5 @@
 # Maintainer: Adityarup Laha <me@adityaruplaha.me>
-# Maintainer: Chris Vittal <chris@vittal.dev>
-_pkgname='plink1.9'
-pkgname="$_pkgname-git"
-# Upstream has changed tag formats, epoch is necessary
-epoch=1
+pkgname='plink1.9'
 _pkgver=1.9
 pkgver=1.9.b.7.11.r64.gacb45ef4
 pkgrel=1
diff --git a/BioArchLinux/plink1.9/bin-name.patch b/BioArchLinux/plink1.9/bin-name.patch
new file mode 100644
index 0000000000..5fb0201d7d
--- /dev/null
+++ b/BioArchLinux/plink1.9/bin-name.patch
@@ -0,0 +1,16 @@
+diff --color -ura src/plink1.9/1.9/Makefile src/plink1.9-patched/1.9/Makefile
+--- src/plink1.9/1.9/Makefile	2024-07-26 14:43:56.962588763 +0530
++++ src/plink1.9-patched/1.9/Makefile	2024-07-26 14:45:39.865461011 +0530
+@@ -77,10 +77,10 @@
+ 
+ all:	$(BIN)
+ 
+-plink: $(OBJS)
++$(BIN): $(OBJS)
+ 	$(CXX) $(OBJS) $(LDFLAGS_EXTRA) $(BLASFLAGS) $(LDFLAGS) $(ZLIB) -o $@
+ 
+-plinkw: $(OBJS)
++$(BIN)w: $(OBJS)
+ 	gfortran -O2 $(OBJS) $(LDFLAGS_EXTRA) -Wl,-Bstatic $(BLASFLAGS) $(LDFLAGS) $(ZLIB) -o $@
+ 
+ install:

From 275969e6c225cc3b981228562906271942db9fd7 Mon Sep 17 00:00:00 2001
From: Adityarup Laha <me@adityaruplaha.me>
Date: Sat, 27 Dec 2025 20:03:58 +0530
Subject: [PATCH 3/4] Use use_max_tag with include_regex instead.

---
 BioArchLinux/plink1.9/lilac.yaml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/BioArchLinux/plink1.9/lilac.yaml b/BioArchLinux/plink1.9/lilac.yaml
index c4375e2f31..f854d64a6d 100644
--- a/BioArchLinux/plink1.9/lilac.yaml
+++ b/BioArchLinux/plink1.9/lilac.yaml
@@ -7,5 +7,6 @@ post_build_script: |
 update_on:
   - source: github
     github: chrchang/plink-ng
-    use_latest_release: true
+    use_max_tag: true
+    include_regex: '^v1.9'
     prefix: 'v'

From 5464dc0b51d08ae21ff279f4ebe025844d1ba3fc Mon Sep 17 00:00:00 2001
From: Adityarup Laha <me@adityaruplaha.me>
Date: Sun, 28 Dec 2025 11:23:31 +0530
Subject: [PATCH 4/4] Fix regex.

---
 BioArchLinux/plink1.9/lilac.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/BioArchLinux/plink1.9/lilac.yaml b/BioArchLinux/plink1.9/lilac.yaml
index f854d64a6d..e90e817a1f 100644
--- a/BioArchLinux/plink1.9/lilac.yaml
+++ b/BioArchLinux/plink1.9/lilac.yaml
@@ -8,5 +8,5 @@ update_on:
   - source: github
     github: chrchang/plink-ng
     use_max_tag: true
-    include_regex: '^v1.9'
+    include_regex: '^v1\.9\..*'
     prefix: 'v'