From e978c365080e8765f234868ad266cd333c53a94f Mon Sep 17 00:00:00 2001
From: V3n3RiX <venerix@koprulu.sector>
Date: Tue, 26 Mar 2024 13:01:14 +0000
Subject: gentoo auto-resync : 26:03:2024 - 13:01:14

---
 sci-libs/Manifest.gz                 | Bin 45146 -> 45147 bytes
 sci-libs/htslib/Manifest             |   2 ++
 sci-libs/htslib/htslib-1.19.1.ebuild |  52 +++++++++++++++++++++++++++++++++++
 3 files changed, 54 insertions(+)
 create mode 100644 sci-libs/htslib/htslib-1.19.1.ebuild

(limited to 'sci-libs')

diff --git a/sci-libs/Manifest.gz b/sci-libs/Manifest.gz
index 1b4d9e8de0ed..bd9af8045530 100644
Binary files a/sci-libs/Manifest.gz and b/sci-libs/Manifest.gz differ
diff --git a/sci-libs/htslib/Manifest b/sci-libs/htslib/Manifest
index c1e1e906205e..ae037d52998f 100644
--- a/sci-libs/htslib/Manifest
+++ b/sci-libs/htslib/Manifest
@@ -1,3 +1,5 @@
 DIST htslib-1.17.tar.bz2 4619884 BLAKE2B c45591b3f1da4f6ddfdf5e1a20864583d57de2a460d42049715335fce7dafe1f5cd14403e6033fee4f9d0bfc75f8777b5835d2d01bf2cadff0155d9fc92b97d9 SHA512 624ab449d57713dab2d34399926c065f8cff8a45e6fbe68e0bb518c601421f587b613caeb095f8639b1d67cdb4a65d658c85f942173bcaa48da026fe15def5d3
+DIST htslib-1.19.1.tar.bz2 4775086 BLAKE2B 3af6770ade9505a3c71f6d522c0971eb77ea2549670043a539a2a4681e583554dc154b9b9fb33f1faa94be336a09945a28c57aa4bcfe0f39b03dd7585c49269a SHA512 a40de47ecae68756c158c1c7b578fa2a5c13bf6f98626e863af31a20d7880ffd415d966280c00bfe726f496d913eb0fcf014dd4beb8c1dbe36ed9735a48bd01e
 EBUILD htslib-1.17.ebuild 1074 BLAKE2B 2bfb261fbe65d7a3d2cd33aec2c3e1e3c649570abfa7b5a630e43f07118869731e22ee1180d8877237aa3423e76c5f3eba7c87c6b1bfe591a982a427eb7d6fc6 SHA512 d2901ebb4f8e43b7db795e6a6e4f53b5eaad3bbc5db5607d65db08f517fbf6c41547053ccf229a6f0849ba38921127233ce824e8d18bcefbd7a921c284703609
+EBUILD htslib-1.19.1.ebuild 1074 BLAKE2B fa229ef5727c85228457d016736c6edf3258b1ea5d94dc2e441d7095bcaf7be20a079ec6f1838889b69f2c492aa3467070e3860ca7da5ce7cc6f12be7540ff1b SHA512 d9bdcd736f6e669f81a0c221666fc349253f1f5b00f1476bba69a4673690b04e0c8f07346c22be4900062b51274e8c1f27a6674b263463dba32f028955504e79
 MISC metadata.xml 342 BLAKE2B 1c27212ba39cbbd235e2b023af977d5dffbb53dab193e21c989b2da52641fec13317110cfb52fd73cbe7fbdd5aa6b3628ee7cd55ae919551fa82267b05f93e2d SHA512 5b61d1b204a33d6328d3964346c48dc35bc4e29c56dc7920a63caf2fc510be35b10f74f2649a2670239de90cff5ed4652fa99d4ef51a55245b7fc4b31f29674b
diff --git a/sci-libs/htslib/htslib-1.19.1.ebuild b/sci-libs/htslib/htslib-1.19.1.ebuild
new file mode 100644
index 000000000000..2a38fa8634c8
--- /dev/null
+++ b/sci-libs/htslib/htslib-1.19.1.ebuild
@@ -0,0 +1,52 @@
+# Copyright 1999-2024 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit toolchain-funcs
+
+DESCRIPTION="C library for high-throughput sequencing data formats"
+HOMEPAGE="http://www.htslib.org/"
+SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2"
+
+LICENSE="MIT"
+SLOT="0/3"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="+bzip2 curl +lzma"
+
+RDEPEND="
+	sys-libs/zlib
+	bzip2? ( app-arch/bzip2 )
+	curl? ( net-misc/curl )
+	lzma? ( app-arch/xz-utils )"
+DEPEND="${RDEPEND}"
+
+src_prepare() {
+	default
+
+	# upstream injects LDFLAGS into the .pc file,
+	# which is a big nono for QA
+	sed -e '/^\(static_l\|Libs.private\|Requires.private\)/d' \
+		-i htslib.pc.in || die
+}
+
+src_configure() {
+	econf \
+		--disable-gcs \
+		--disable-plugins \
+		--disable-s3 \
+		$(use_enable bzip2 bz2) \
+		$(use_enable curl libcurl) \
+		$(use_enable lzma)
+}
+
+src_compile() {
+	emake AR="$(tc-getAR)"
+}
+
+src_install() {
+	default
+
+	# doesn't use libtool, can't disable static libraries
+	find "${ED}" -name '*.a' -delete || die
+}
-- 
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