From 9ecc5c74ec830cfe4498f8be2f151f6fdc43945e Mon Sep 17 00:00:00 2001
From: Saba Gogichaishvili <sd.gogich@gmail.com>
Date: Wed, 11 Aug 2021 15:05:37 +0400
Subject: [PATCH 1/3] New package: htslib-1.13

---
 common/shlibs           |  1 +
 srcpkgs/htslib-devel    |  1 +
 srcpkgs/htslib/template | 29 +++++++++++++++++++++++++++++
 3 files changed, 31 insertions(+)
 create mode 120000 srcpkgs/htslib-devel
 create mode 100644 srcpkgs/htslib/template

diff --git a/common/shlibs b/common/shlibs
index 278d2456072f..4f4d9cc4aa7c 100644
--- a/common/shlibs
+++ b/common/shlibs
@@ -4004,3 +4004,4 @@ liblhasa.so.0 lhasa-0.3.1_2
 libmt32emu.so.2 libmt32emu-2.5.1_1
 libqrtr-glib.so.0 libqrtr-glib-1.0.0_1
 libstemmer.so.2 libstemmer-2.1.0_1
+libhts.so.3 htslib-1.13_1
diff --git a/srcpkgs/htslib-devel b/srcpkgs/htslib-devel
new file mode 120000
index 000000000000..9786daad45dd
--- /dev/null
+++ b/srcpkgs/htslib-devel
@@ -0,0 +1 @@
+htslib
\ No newline at end of file
diff --git a/srcpkgs/htslib/template b/srcpkgs/htslib/template
new file mode 100644
index 000000000000..9a3b1413caf7
--- /dev/null
+++ b/srcpkgs/htslib/template
@@ -0,0 +1,29 @@
+# Template file for 'htslib'
+pkgname=htslib
+version=1.13
+revision=1
+build_style=gnu-configure
+makedepends="zlib-devel bzip2-devel liblzma-devel libcurl-devel openssl-devel"
+checkdepends="perl"
+short_desc="C library for high-throughput sequencing data formats"
+maintainer="Saba Gogichaishvili <sd.gogich@gmail.com>"
+license="MIT"
+homepage="https://www.htslib.org/"
+distfiles="https://github.com/samtools/htslib/releases/download/${version}/htslib-${version}.tar.bz2"
+checksum=f2407df9f97f0bb6b07656579e41a1ca5100464067b6b21bf962a2ea4b0efd65
+
+post_install() {
+	vlicense LICENSE
+}
+
+htslib-devel_package() {
+	depends="${sourcepkg}>=${version}_${revision}"
+	short_desc+=" - development files"
+	pkg_install() {
+		vmove usr/include
+		vmove usr/lib/pkgconfig
+		vmove "usr/lib/*.a"
+		vmove "usr/lib/*.so"
+		vmove usr/share
+	}
+}

From bc50b4a5e3ff961f7b8f5f6524a1bed9d49f9574 Mon Sep 17 00:00:00 2001
From: Saba Gogichaishvili <sd.gogich@gmail.com>
Date: Wed, 11 Aug 2021 15:05:56 +0400
Subject: [PATCH 2/3] New package: bcftools-1.13

---
 srcpkgs/bcftools/template | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)
 create mode 100644 srcpkgs/bcftools/template

diff --git a/srcpkgs/bcftools/template b/srcpkgs/bcftools/template
new file mode 100644
index 000000000000..ea74811827e4
--- /dev/null
+++ b/srcpkgs/bcftools/template
@@ -0,0 +1,18 @@
+# Template file for 'bcftools'
+pkgname=bcftools
+version=1.13
+revision=1
+build_style=gnu-configure
+configure_args="--with-htslib=system --enable-perl-filters --enable-libgsl"
+makedepends="htslib-devel zlib-devel gsl-devel perl"
+short_desc="Read/write BCF2/VCF/gVCF files and call/filter/sum SNP and short indels"
+maintainer="Saba Gogichaishvili <sd.gogich@gmail.com>"
+license="MIT"
+homepage="https://www.htslib.org/"
+distfiles="https://github.com/samtools/bcftools/releases/download/${version}/bcftools-${version}.tar.bz2"
+checksum=13bfa1da2a5edda8fa51196a47a0b4afb3fef17516451e4f0e78477f3dd30b90
+python_version=3
+
+post_install() {
+	vlicense LICENSE
+}

From 4e28e07cef3235ebc15d4221cd2dc10d66c3971f Mon Sep 17 00:00:00 2001
From: Saba Gogichaishvili <sd.gogich@gmail.com>
Date: Wed, 11 Aug 2021 15:06:01 +0400
Subject: [PATCH 3/3] New package: samtools-1.13

---
 srcpkgs/samtools/template | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)
 create mode 100644 srcpkgs/samtools/template

diff --git a/srcpkgs/samtools/template b/srcpkgs/samtools/template
new file mode 100644
index 000000000000..0d2ebb6f39f2
--- /dev/null
+++ b/srcpkgs/samtools/template
@@ -0,0 +1,18 @@
+# Template file for 'samtools'
+pkgname=samtools
+version=1.13
+revision=1
+build_style=gnu-configure
+configure_args="--with-htslib=system"
+makedepends="htslib-devel zlib-devel ncurses-devel"
+checkdepends="perl"
+short_desc="Read/write/edit/index/view SAM/BAM/CRAM files"
+maintainer="Saba Gogichaishvili <sd.gogich@gmail.com>"
+license="MIT"
+homepage="https://www.htslib.org/"
+distfiles="https://github.com/samtools/samtools/releases/download/${version}/samtools-${version}.tar.bz2"
+checksum=616ca2e051cc8009a1e9c01cfd8c7caf8b70916ddff66f3b76914079465f8c60
+
+post_install() {
+	vlicense LICENSE
+}