gentoo auto-resync : 25:05:2024 - 00:07:14

13 files changed, 76 insertions, 93 deletions

diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz
index 90ea37bf4b0d..b00432ffd6cc 100644
--- a/sci-biology/Manifest.gz
+++ b/sci-biology/Manifest.gz
diff --git a/sci-biology/bcftools/Manifest b/sci-biology/bcftools/Manifest
index 9d0ed7aa0212..5ae9c11fe860 100644
--- a/sci-biology/bcftools/Manifest
+++ b/sci-biology/bcftools/Manifest
@@ -1,5 +1,5 @@
-DIST bcftools-1.17.tar.bz2 7538043 BLAKE2B 82f65d53ebea0527ff000329f158ebdb1d603e04841a096cf8ca0434e7a5694ab43da7959ee10e9cb29328bf82301c03200e1203578a74e2e1118856b2641502 SHA512 39ae44a682e626a5261900e9412170a269e460b559d6607db697e6a12b1e512ffb3bdeb3486413e19b8adca26a8ccbb2bd4af24459decb74592c54473d2c6a68
 DIST bcftools-1.19.tar.bz2 7906216 BLAKE2B 43e7ac0fc6ffcf837607fb2fbbd58a72106a89b018d1fd4b24db0eb854a9bf0efd0c7762fae84bf7f51226346777be646d134159ea48e3eb3df71799e9353a3f SHA512 a203c65fa58fca8fb5276e73ed8fc23dfd841e9dc05881304a8b91327d60ac3b5fcf5a55a1f1bab5647037f037ff30f2881791052f6e29cf38c646cbc947a746
-EBUILD bcftools-1.17.ebuild 900 BLAKE2B 98f04325ca039867010c25c5ebff64725de637960c1980cce0faee7b8514d187ca3a309a3db79bb809ebcb9938869884c89b54f232fcf826aa34b38c5dde9c6e SHA512 82bb9a379019f0d9f9c601fad06d4041e5b890cb21618cc37f37f5f6ce0c3d5d9cd1d6223a19b8a53303e8ab3ce4046a21fbd3b7b18fd45243d57226d040ffc4
+DIST bcftools-1.20.tar.bz2 7883049 BLAKE2B 36bfd82c9500f384b75ef93242a5879123f7fd63c893c95a1ce5efbfa9396f2c1fd75025ea2dd48d37e7dc93426ffaffbb2f3c6bdf64128fbdd3af2a2f760b17 SHA512 c77294923a6bb5cb97a2c4947e79aa215612a62f71ba0e4dde627cd3d97ee9a28a3682e8ab2f3bedd0e75e2bb9800915d9430f9504f09ead4492d3583553db2a
 EBUILD bcftools-1.19.ebuild 901 BLAKE2B 401502d51a1b537d791355000f38403239ca57b41473cb58e1dcd3ab4057582fb19bec5d493df318386fe7c45337046e813a148d44ea0dda49468662d0567570 SHA512 b97efeaccdf86b37e714ff3f0e260f12927fa32eda3376b981d10ce7527b4da8f479e6b049386582e843329fa8e3d5a15236724e5a137d44219d1ebceca38097
+EBUILD bcftools-1.20.ebuild 901 BLAKE2B 401502d51a1b537d791355000f38403239ca57b41473cb58e1dcd3ab4057582fb19bec5d493df318386fe7c45337046e813a148d44ea0dda49468662d0567570 SHA512 b97efeaccdf86b37e714ff3f0e260f12927fa32eda3376b981d10ce7527b4da8f479e6b049386582e843329fa8e3d5a15236724e5a137d44219d1ebceca38097
 MISC metadata.xml 344 BLAKE2B 37f8e82e8a5a9ad572580a7e5ae6daa6911d672f17b8526f81b236cbc2e50a32c4cd2566aaed9f5feee016d7e2de7db2a40b60616e86c3e8cae307d60cebc70e SHA512 0160c9606089d610613d71dc0aa9c9c5e5266483fdc9c407b6e0ed911eac8f8b32ffaf5a49bbb427393c8240e9868df51f0fc68b2f45467f65d9b3d54b0ddde1
diff --git a/sci-biology/bcftools/bcftools-1.17.ebuild b/sci-biology/bcftools/bcftools-1.20.ebuild
index 6adee705bb46..27d474fe35f9 100644
--- a/sci-biology/bcftools/bcftools-1.17.ebuild
+++ b/sci-biology/bcftools/bcftools-1.20.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2023 Gentoo Authors
+# Copyright 1999-2024 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=8
 
-PYTHON_COMPAT=( python3_{9..11} )
+PYTHON_COMPAT=( python3_{10..12} )
 
 inherit python-single-r1
 
diff --git a/sci-biology/pysam/Manifest b/sci-biology/pysam/Manifest
index 4a490595f41b..5c166b78848f 100644
--- a/sci-biology/pysam/Manifest
+++ b/sci-biology/pysam/Manifest
@@ -1,5 +1,4 @@
-AUX pysam-0.21.0-cython-3.patch 946 BLAKE2B 6b74b084d4f0308a77266c748209a91aa23fc0f51635b45bb2e47efc7d1e2f4a67993305d0f12c74964add24ec49ebb8b56bff720aec065a76257bda5a677cdb SHA512 763bee599547059dfff39f7ae087402dfca67acabc048012663d6cd792c605d6dc07210f777d22e9373c086cd9cd468e7ae3060a501962157ba5f6971c8033a1
-DIST pysam-0.21.0.gh.tar.gz 3842829 BLAKE2B 83db290ec0bae71106276ed4f1721292c0d2fa55053c7451f0a8a79619b1c4d8444b99293ac5d8051bfb0b59e984e32a89798bab091e3a019b7c2a3fb7414d1c SHA512 b2ac986b6a352df1d2066a224d710648a88d8ad44273623a89ae0f4bb2645b00f0d0e1685c8ccedfd379259255957e653f3c3199621ac1d4c26098f538b6bfa7
-EBUILD pysam-0.21.0.ebuild 1744 BLAKE2B d6211a396810673da6392e4377a412bc6886c5eb9d5ad45ae85b278ae9d2202c4a706186b64ae3b1ae88fc0b32c532dad494bf69757b3c66dbf96e7001b48d2a SHA512 41be02962a1af5463dcc4ca98ec2af0e6986ec8d8a8101b813954754865c95d75f5f8a0ae20d3c76465475aa94e30fade45734931221eea01ab05cb7746acfce
+DIST pysam-0.22.1.gh.tar.gz 3885851 BLAKE2B 6f83c445c7e63e28823f443b0f106726303b0609f4040e9dca930c820d48c2adfe13d33ecffb514ce75c3b03968af050652689a0be39aaabca1af546e9188480 SHA512 fb8dc7c4a6ae908d8d409789f2706cce589d4b6a1057bcc4043f8a26a5b390f79d30d1a1cbe69cbf370caabf261ed8367685393240765080e94f1782ed7f0350
+EBUILD pysam-0.22.1.ebuild 1648 BLAKE2B 9d0c666e39b48dea088445a0959d364892f9b2a3e90664788f214ac66df709c70eaaf8c90240488a4c948409f0548641f4d511af983037b3afc481444621f7fb SHA512 e35adedadd3c3726eb817c85f225fc2715eccdcd0c2bed5c11f749d07a7e99b2f28fee0244bd64f1383329d20edb7a2364112483af8a814b447b29fc3d1b762b
 EBUILD pysam-9999.ebuild 1709 BLAKE2B b7297d21abf0e581c5c2d8a72a7e6805cb5f96f6e878cc979fc0f5a34e57bdd25a2f50abaa9ee10040559e66ee42d3a24696a7093103658175b27858acaac95c SHA512 7e7a782243897a89a3539b3eb79ccd0790c6b0afcf79453526c30371f867faaf8eca6454e64d3bea250ff13753ff400fe5ff3352c080c85285cafa2346e3564a
 MISC metadata.xml 442 BLAKE2B e3d339868a09d8930ff6d83f414f8166ed283a66d83d5b0fed0031024db151b17b1347f5e015f2b9c2152a041e2beb70696362be9b4e3fc225078bc5c520ad58 SHA512 4b1d08c5524e1bb04129e0d38f0584654b34979024afd2cf15bd482654ca8fac9c82e6db0661f7370f9fefa6949f1291ba3c18a9dca5d5041bd6f76554fa33c7
diff --git a/sci-biology/pysam/files/pysam-0.21.0-cython-3.patch b/sci-biology/pysam/files/pysam-0.21.0-cython-3.patch
deleted file mode 100644
index 303a4fb0dcdc..000000000000
--- a/sci-biology/pysam/files/pysam-0.21.0-cython-3.patch
+++ /dev/null
@@ -1,24 +0,0 @@
-From 17bb13dcfdb56ac238458dcef23fe01893a892e9 Mon Sep 17 00:00:00 2001
-From: John Marshall <jmarshall@hey.com>
-Date: Sat, 8 Apr 2023 11:00:46 +1200
-Subject: [PATCH] Remove incorrect type annotation
-
-The annotation already in pysam/libcbcf.pyi is correct.
-Fixes #1179 as reopened on April 6th.
----
- pysam/libcbcf.pyx | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/pysam/libcbcf.pyx b/pysam/libcbcf.pyx
-index 8c088af2..8ecfe5f3 100644
---- a/pysam/libcbcf.pyx
-+++ b/pysam/libcbcf.pyx
-@@ -3479,7 +3479,7 @@ cdef class VariantRecordSample(object):
-         return bcf_format_get_alleles(self)
- 
-     @alleles.setter
--    def alleles(self, value: tuple):
-+    def alleles(self, value):
-         # Sets the genotype, supply a tuple of alleles to set.
-         # The supplied alleles need to be defined in the correspoding pysam.libcbcf.VariantRecord
-         # The genotype is reset when an empty tuple, None or (None,) is supplied
diff --git a/sci-biology/pysam/pysam-0.21.0.ebuild b/sci-biology/pysam/pysam-0.22.1.ebuild
index 77292ed29613..9070476873e1 100644
--- a/sci-biology/pysam/pysam-0.21.0.ebuild
+++ b/sci-biology/pysam/pysam-0.22.1.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2023 Gentoo Authors
+# Copyright 1999-2024 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=8
 
-PYTHON_COMPAT=( python3_{9..11} )
+PYTHON_COMPAT=( python3_{10..12} )
 
 inherit distutils-r1
 
@@ -17,30 +17,26 @@ LICENSE="MIT"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
 
-RDEPEND="=sci-libs/htslib-1.17*:="
+RDEPEND="=sci-libs/htslib-1.20*:="
 DEPEND="${RDEPEND}
-	dev-python/cython[${PYTHON_USEDEP}]
 	dev-python/setuptools[${PYTHON_USEDEP}]"
 BDEPEND="
+	dev-python/cython[${PYTHON_USEDEP}]
 	test? (
-		=sci-biology/bcftools-1.17*
-		=sci-biology/samtools-1.17*
+		=sci-biology/bcftools-1.20*
+		=sci-biology/samtools-1.20*
 	)"
 
 distutils_enable_tests pytest
 
 DISTUTILS_IN_SOURCE_BUILD=1
 
-PATCHES=(
-	# backport
-	# https://github.com/pysam-developers/pysam/commit/17bb13dcfdb56ac238458dcef23fe01893a892e9
-	"${FILESDIR}"/${P}-cython-3.patch
-)
-
 EPYTEST_DESELECT=(
 	# only work with bundled htslib
 	'tests/tabix_test.py::TestRemoteFileHTTP'
 	'tests/tabix_test.py::TestRemoteFileHTTPWithHeader'
+
+	'tests/AlignedSegment_test.py::TestBaseModifications'
 )
 
 python_prepare_all() {
diff --git a/sci-biology/raxml/Manifest b/sci-biology/raxml/Manifest
index 820b570e7e04..cc69c7639d9b 100644
--- a/sci-biology/raxml/Manifest
+++ b/sci-biology/raxml/Manifest
@@ -1,4 +1,4 @@
-AUX raxml-7.2.6-makefile.patch 786 BLAKE2B d6fc28b20fc3b00b33cefd93fa90f0db255eec642a3fd760baa5489ab90dbb31d9896fe7a595e9f2e4e47b53ab24e1ef2a80486dbe77062f835fce17687a50ae SHA512 955c1403dbae7d5308f10808c3689d04cd4bc6166647fd5d7c6a5eafca45b42f409a22642a57dc19a8f3ce4e00e2e554988ed5a02954ee85ab805759e60beeea
-DIST RAxML-7.2.6.tar.bz2 202803 BLAKE2B 579676ff9fad1563eabb9507015acff010977a89ae087df9b828b80bc9352ed44c98faeaf4c8d884ffa14176bfa28772dc9872ad8b5d401aff8b834c728e5f65 SHA512 b0027a7e583e6471a774d9e784a0be1ff63b3824a8cfbebca68bf9e414adab297206ea2d43c9b97456e6acc0a6a15f55ca33983381dd6150f9e7ea71ddecdcd3
-EBUILD raxml-7.2.6.ebuild 902 BLAKE2B 23d2b1a93bf50587d5bcacbaf261ad98eecd4e6d6d86bce62bad4459286bdb678c60ad5699cd22c5d6e03df4fb49ccd95c40bbb30f6ec7990e8f81518709aa66 SHA512 5583a0fcb21f80f1cc1d7fe282f56235b6b0add1699330652f8c6c669cbbb1975eb8e088f566252b897a94e5bb80f2738de538d570951bd7508b5a607324c34f
-MISC metadata.xml 268 BLAKE2B a4d67334cdad8626d60e46b677ee1c83f569e5e20b3739a7664bb33be1829f8478af35e135bf734a6ff151b8543ea6c4ecafbf822cee8189f7e7096bd9698711 SHA512 59d3d8213b1a219396b74b6f4188c01e1cb4eb1c63e6792ce1e7fdb8000d1a4625919337ff77288ca7f7e07d9753f481d2381a06f554012633cd678194c980de
+AUX raxml-8.2.13-makefile.patch 1996 BLAKE2B 4c11992d1d8575ed54f5b374d7344a7de21dbec2eabb78a74ad894662c3008e2692724a3f7ac9659928bdb0e75a3fd4b6ad3d8c729ebb0ad0dd91c52cfe65d81 SHA512 044adeb9d66f1b8ba628c39914442c57b933957bca73ff856d00963878e8f1055baaf51e4feffb78e3090c7b445f819be3418440fd793340b6e8f65eb80b0e18
+DIST raxml-8.2.13.tar.gz 10201721 BLAKE2B ee48dc599947619d12a54cafef1eee554abc0df30a31ba2fdb501b228dadec9f137acff8f472047f4686304f74d27893696c95ff808baa128c2c3d83539366a1 SHA512 c99dc3f8c8798cda38c644501f474c0261e72c1f3b64d594d5006fa03e8d8c4da3bdf20b8e3c6c9f669c9509d5af27a0c286a2570a54c8ff7df7cd63c1f78885
+EBUILD raxml-8.2.13.ebuild 921 BLAKE2B 2facbdad60a72dc69341aafb8389e28196ba4ef7a9e3bbd71bcb7d0c3f3daedf7bd844798a4456a05344ad80a900936e73a914cee4cfa40d08a47a559aac8036 SHA512 6f2a3e357187c8ec081cd2be94c487263f062cc502e39a77e3c15fad1dad1b3a97ecfa84c2660d2a4a43a12a06bd8547a4710b0ce187dcf11dfab0269cf62e44
+MISC metadata.xml 350 BLAKE2B 7cf3cb5ea8626cadeb2a4709f466742bb1d909c58717aa0988bb4157203db26a7e571d1aec74e1bb73703bcba3f00c6d828d32ea342709a4244f4235bf2313c0 SHA512 6738c142066459babe699d53089935c7c2c1864951cf6a3148beb9015a67ce0dc60e70caa169348126b5b44f7f693b95810b871debacccd91a2643e03820f2ea
diff --git a/sci-biology/raxml/files/raxml-7.2.6-makefile.patch b/sci-biology/raxml/files/raxml-7.2.6-makefile.patch
deleted file mode 100644
index 6b82ed65b770..000000000000
--- a/sci-biology/raxml/files/raxml-7.2.6-makefile.patch
+++ /dev/null
@@ -1,29 +0,0 @@
- Makefile.gcc |    6 +++---
- 1 files changed, 3 insertions(+), 3 deletions(-)
-
-diff --git a/Makefile.gcc b/Makefile.gcc
-index 716b6c6..f0c1de2 100644
---- a/Makefile.gcc
-+++ b/Makefile.gcc
-@@ -1,10 +1,10 @@
- # Makefile August 2006 by Alexandros Stamatakis
- # Makefile cleanup October 2006, Courtesy of Peter Cordes <peter@cordes.ca>
- 
--CC = gcc 
-+CC ?= gcc 
- 
- 
--CFLAGS = -D_GNU_SOURCE  -fomit-frame-pointer -funroll-loops -O2 -msse
-+CPPFLAGS += -D_GNU_SOURCE
- 
- 
- 
-@@ -19,7 +19,7 @@ all : raxmlHPC
- GLOBAL_DEPS = axml.h globalVariables.h
- 
- raxmlHPC : $(objs)
--	$(CC) -o raxmlHPC $(objs) $(LIBRARIES) 
-+	$(CC) $(LDFLAGS) -o raxmlHPC $(objs) $(LIBRARIES) $(LIBS)
- 
- classify.o : classify.c $(GLOBAL_DEPS)
- evaluatePartialSpecialGeneric.o : evaluatePartialSpecialGeneric.c $(GLOBAL_DEPS)
diff --git a/sci-biology/raxml/files/raxml-8.2.13-makefile.patch b/sci-biology/raxml/files/raxml-8.2.13-makefile.patch
new file mode 100644
index 000000000000..d774b1fb824d
--- /dev/null
+++ b/sci-biology/raxml/files/raxml-8.2.13-makefile.patch
@@ -0,0 +1,37 @@
+--- a/Makefile.gcc
++++ b/Makefile.gcc
+@@ -1,7 +1,6 @@
+ # Makefile August 2006 by Alexandros Stamatakis
+ # Makefile cleanup October 2006, Courtesy of Peter Cordes <peter@cordes.ca>
+ 
+-CC = gcc 
+ 
+ ARCH := $(shell uname -m)
+ ifeq ($(ARCH), x86_64)
+@@ -10,7 +9,7 @@
+ ARCH_CFLAGS=
+ endif
+ 
+-CFLAGS = -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 $(ARCH_CFLAGS) #-Wall -Wunused-parameter -Wredundant-decls  -Wreturn-type  -Wswitch-default -Wunused-value -Wimplicit  -Wimplicit-function-declaration  -Wimplicit-int -Wimport  -Wunused  -Wunused-function  -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast  -Wmissing-declarations -Wmissing-prototypes  -Wnested-externs  -Wold-style-definition -Wstrict-prototypes -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value  -Wunused-variable -Wformat  -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast
++CFLAGS += -D_GNU_SOURCE #-Wall -Wunused-parameter -Wredundant-decls  -Wreturn-type  -Wswitch-default -Wunused-value -Wimplicit  -Wimplicit-function-declaration  -Wimplicit-int -Wimport  -Wunused  -Wunused-function  -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast  -Wmissing-declarations -Wmissing-prototypes  -Wnested-externs  -Wold-style-definition -Wstrict-prototypes -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value  -Wunused-variable -Wformat  -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast
+ 
+ LIBRARIES = -lm
+ 
+@@ -23,7 +22,7 @@
+ GLOBAL_DEPS = axml.h globalVariables.h rmq.h rmqs.h #mem_alloc.h
+ 
+ raxmlHPC : $(objs)
+-	$(CC) -o raxmlHPC $(objs) $(LIBRARIES) $(LDFLAGS) 
++	$(CC) $(CFLAGS) $(LDFLAGS) -o raxmlHPC $(objs) $(LIBRARIES)
+ 
+ rmqs.o : rmqs.c $(GLOBAL_DEPS)
+ classify.o : classify.c $(GLOBAL_DEPS)
+@@ -51,8 +50,6 @@
+ 
+ 
+ 
+-eigen.o : eigen.c $(GLOBAL_DEPS)
+-	$(CC) -c -o eigen.o eigen.c 
+ clean : 
+ 	$(RM) *.o raxmlHPC
+ 
diff --git a/sci-biology/raxml/metadata.xml b/sci-biology/raxml/metadata.xml
index ccdff086e20b..dd68d972db31 100644
--- a/sci-biology/raxml/metadata.xml
+++ b/sci-biology/raxml/metadata.xml
@@ -1,8 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
+	<maintainer type="project">
+		<email>sci-biology@gentoo.org</email>
+		<name>Gentoo Biology Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">stamatak/standard-RAxML</remote-id>
+	</upstream>
 </pkgmetadata>
diff --git a/sci-biology/raxml/raxml-7.2.6.ebuild b/sci-biology/raxml/raxml-8.2.13.ebuild
index adb044426381..859016195389 100644
--- a/sci-biology/raxml/raxml-7.2.6.ebuild
+++ b/sci-biology/raxml/raxml-8.2.13.ebuild
@@ -1,29 +1,30 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2024 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=7
+EAPI=8
 
 inherit flag-o-matic toolchain-funcs
 
 DESCRIPTION="Sequential, Parallel & Distributed Inference of Large Phylogenetic Trees"
-HOMEPAGE="http://wwwkramer.in.tum.de/exelixis/software.html"
-SRC_URI="http://wwwkramer.in.tum.de/exelixis/software/RAxML-${PV}.tar.bz2"
-S="${WORKDIR}/RAxML-${PV}"
+HOMEPAGE="https://github.com/stamatak/standard-RAxML"
+SRC_URI="https://github.com/stamatak/standard-RAxML/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/standard-RAxML-${PV}"
 
 LICENSE="GPL-2"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
 IUSE="cpu_flags_x86_sse3 +threads"
-REQUIRED_USE="cpu_flags_x86_sse3"
 
 # mpi is not supported in version 7.2.2. mpi is enabled by adding -DPARALLEL to CFLAGS
 PATCHES=( "${FILESDIR}"/${P}-makefile.patch )
 
 src_configure() {
-	use cpu_flags_x86_sse3 && append-cppflags -D__SIM_SSE3
-	use threads && \
-		append-cppflags -D_USE_PTHREADS && \
-		append-libs -pthread
+	use cpu_flags_x86_sse3 &&
+		append-cppflags -D__SIM_SSE3 &&
+		append-cflags -msse3
+	use threads &&
+		append-cppflags -D_USE_PTHREADS &&
+		append-cflags -pthread
 
 	tc-export CC
 }
diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest
index add06bedafa2..67b2c2142193 100644
--- a/sci-biology/samtools/Manifest
+++ b/sci-biology/samtools/Manifest
@@ -1,5 +1,5 @@
-DIST samtools-1.17.tar.bz2 8605080 BLAKE2B 09cb0bff7bf7113a77f57fdb879765b28b65461a574e4a1ab20ae2327af46e5616e04f03eb68706d42ba0643e887d7921974a3d78c5f87d296a4c3b691215260 SHA512 107a6df858c6bd2556ba4e86cc1922c3184df095f347039fa94bfd24e5ee21e1a4a9fba5a7cce248a06ad47f99978d9aae570efee7e30e165f33ea848a2cd3c3
 DIST samtools-1.19.2.tar.bz2 9150483 BLAKE2B fb845b2ccd61f1731ef4cdc180f4b9a4ac75e8c73c1ceaa9409b99e8052ca66b88c73fc71fd1067942aa24964f6df8dcb2d93631e5757e0cc200d7a3b9fad461 SHA512 c08d729fed21112855e0acc9cf7f29c7670d38a02ad6b0f2e9b9ef15a18f07e3e194cc4f6913481c98cd3e85dd4dc975dac96155b892da58bbe8ea3679a5270f
-EBUILD samtools-1.17.ebuild 926 BLAKE2B c2baac0d68599fadfc1825e2c0046c0596d50cedd15e6859bbfffbd3d735ae6dca2e873d835120da7be8a9c91ce17dd449010dfa956899de69c807da0cc60c7c SHA512 d43c9a9da338c0820f0237925895684077a2df428be3892f3433f050c3082d605a1edefdb265ded6f123eed491dc05578d4e46177eb79d7fdad3eebc710e3764
+DIST samtools-1.20.tar.bz2 9179938 BLAKE2B b534e659899a822e191c779a6ce9247854036da3435a0b63748783edc96d610ff0f02f73bbb5c1eab3ff86dbcca331113f3312a7c3376141ef89b6a8684446e4 SHA512 8526286243d057758cb846311d0a8c728026d31438e87fcc03e0df576f33bcc6da0e18bce141dbdc438a116341c94aa92701cdf10ba6b1301eadedbb34120822
 EBUILD samtools-1.19.2.ebuild 926 BLAKE2B a9acf64c51c87cf5d913982d22dba55901111ed1802f5795b0a1bd66979b600d815ee37c29aae83bc2d58c73a61330a4ada70fac4192022d23add1bdc89cf26c SHA512 ab73ecba708535299d9cbfc3c02a6efb292b9c85658247a7eba37b915776493027a2ca98de2e8bfe373a667119a06629a3a86f97eded244b7722887c685710c2
+EBUILD samtools-1.20.ebuild 926 BLAKE2B a9acf64c51c87cf5d913982d22dba55901111ed1802f5795b0a1bd66979b600d815ee37c29aae83bc2d58c73a61330a4ada70fac4192022d23add1bdc89cf26c SHA512 ab73ecba708535299d9cbfc3c02a6efb292b9c85658247a7eba37b915776493027a2ca98de2e8bfe373a667119a06629a3a86f97eded244b7722887c685710c2
 MISC metadata.xml 409 BLAKE2B c94eab9ebda4844beb471694106e353ccbbaca53e69de680301c6cfab3f3b6224ec94fcd631c9de2811d309463e5ee6decf2e443bfc68921f3362c6a312cd3af SHA512 fb2d3686e1ee70e4e80266a26603b3e52b680b1537a4569493a3a0511b93e2acdb2be3136df7ae54905a9f86fb7e53fa054607262751ebd8f54903f1905dad24
diff --git a/sci-biology/samtools/samtools-1.17.ebuild b/sci-biology/samtools/samtools-1.20.ebuild
index e105621c7865..42879b0f8698 100644
--- a/sci-biology/samtools/samtools-1.17.ebuild
+++ b/sci-biology/samtools/samtools-1.20.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2023 Gentoo Authors
+# Copyright 1999-2024 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=8