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gnu: bcftools: Update to 1.8.
* gnu/packages/bioinformatics.scm (bcftools): Update to 1.8. * gnu/local.mk: Remove patch. * gnu/packages/patches/bcftools-regidx-unsigned-char.patch: Remove file.
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8df0267ad4
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3 changed files with 3 additions and 21 deletions
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@ -575,7 +575,6 @@ dist_patch_DATA = \
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%D%/packages/patches/azr3.patch \
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%D%/packages/patches/azr3.patch \
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%D%/packages/patches/bash-completion-directories.patch \
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%D%/packages/patches/bash-completion-directories.patch \
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%D%/packages/patches/bazaar-CVE-2017-14176.patch \
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%D%/packages/patches/bazaar-CVE-2017-14176.patch \
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%D%/packages/patches/bcftools-regidx-unsigned-char.patch \
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%D%/packages/patches/binutils-ld-new-dtags.patch \
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%D%/packages/patches/binutils-ld-new-dtags.patch \
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%D%/packages/patches/binutils-loongson-workaround.patch \
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%D%/packages/patches/binutils-loongson-workaround.patch \
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%D%/packages/patches/blast+-fix-makefile.patch \
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%D%/packages/patches/blast+-fix-makefile.patch \
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@ -285,7 +285,7 @@ BAM files.")
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(define-public bcftools
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(define-public bcftools
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(package
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(package
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(name "bcftools")
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(name "bcftools")
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(version "1.5")
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(version "1.8")
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(source (origin
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(source (origin
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(method url-fetch)
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(method url-fetch)
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(uri (string-append
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(uri (string-append
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@ -293,12 +293,11 @@ BAM files.")
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version "/bcftools-" version ".tar.bz2"))
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version "/bcftools-" version ".tar.bz2"))
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(sha256
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(sha256
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(base32
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(base32
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"0093hkkvxmbwfaa7905s6185jymynvg42kq6sxv7fili11l5mxwz"))
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"1vgw2mwngq20c530zim52zvgmw1lci8rzl33pvh44xqk3xlzvjsa"))
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(patches (search-patches "bcftools-regidx-unsigned-char.patch"))
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(modules '((guix build utils)))
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(modules '((guix build utils)))
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(snippet
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(snippet
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;; Delete bundled htslib.
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;; Delete bundled htslib.
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'(delete-file-recursively "htslib-1.5"))))
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'(delete-file-recursively "htslib-1.8"))))
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(build-system gnu-build-system)
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(build-system gnu-build-system)
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(arguments
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(arguments
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`(#:test-target "test"
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`(#:test-target "test"
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@ -1,16 +0,0 @@
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Description: Fix test-regidx argument parsing on archs with unsigned char
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On architectures where char is unsigned "c >= 0" was always true.
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Author: Adrian Bunk <bunk@debian.org>
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Bug-Debian: https://bugs.debian.org/865060
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--- a/test/test-regidx.c
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+++ b/test/test-regidx.c
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@@ -336,7 +336,7 @@
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{"seed",1,0,'s'},
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{0,0,0,0}
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};
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- char c;
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+ int c;
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int seed = (int)time(NULL);
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while ((c = getopt_long(argc, argv, "hvs:",loptions,NULL)) >= 0)
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{
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