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[pkgsrc/trunk]: pkgsrc/biology biology/htslib: Update to 1.12



details:   https://anonhg.NetBSD.org/pkgsrc/rev/523f46b9982b
branches:  trunk
changeset: 449074:523f46b9982b
user:      bacon <bacon%pkgsrc.org@localhost>
date:      Sat Mar 20 18:17:07 2021 +0000

description:
biology/htslib: Update to 1.12
biology/bcftools: Update to 1.12
biology/samtools: Update to 1.12

Numerous enhancements, performance improvements, and bug fixes since 1.10
Minimized pkgsrc patches in all three packages
Moved htslib to custom tarball since Github-generated distfiles are incomplete

diffstat:

 biology/bcftools/Makefile                             |   5 +-
 biology/bcftools/PLIST                                |   6 +-
 biology/bcftools/distinfo                             |  13 +-
 biology/bcftools/patches/patch-Makefile               |  53 +-----------
 biology/bcftools/patches/patch-misc_run-roh.pl        |  24 -----
 biology/htslib/Makefile                               |  10 +-
 biology/htslib/PLIST                                  |   4 +-
 biology/htslib/buildlink3.mk                          |   4 +-
 biology/htslib/distinfo                               |  13 +-
 biology/htslib/patches/patch-Makefile                 |  76 ------------------
 biology/htslib/patches/patch-cram_open__trace__file.c |  18 ----
 biology/htslib/patches/patch-hfile__libcurl.c         |  78 -------------------
 biology/samtools/Makefile                             |   7 +-
 biology/samtools/PLIST                                |   7 +-
 biology/samtools/distinfo                             |  12 +-
 biology/samtools/patches/patch-Makefile               |  44 +---------
 16 files changed, 53 insertions(+), 321 deletions(-)

diffs (truncated from 566 to 300 lines):

diff -r c60e89e20eb4 -r 523f46b9982b biology/bcftools/Makefile
--- a/biology/bcftools/Makefile Sat Mar 20 15:49:07 2021 +0000
+++ b/biology/bcftools/Makefile Sat Mar 20 18:17:07 2021 +0000
@@ -1,7 +1,6 @@
-# $NetBSD: Makefile,v 1.9 2020/12/04 20:45:00 nia Exp $
+# $NetBSD: Makefile,v 1.10 2021/03/20 18:17:07 bacon Exp $
 
-DISTNAME=      bcftools-1.10.2
-PKGREVISION=   2
+DISTNAME=      bcftools-1.12
 CATEGORIES=    biology
 MASTER_SITES=  ${MASTER_SITE_GITHUB:=samtools/}
 
diff -r c60e89e20eb4 -r 523f46b9982b biology/bcftools/PLIST
--- a/biology/bcftools/PLIST    Sat Mar 20 15:49:07 2021 +0000
+++ b/biology/bcftools/PLIST    Sat Mar 20 18:17:07 2021 +0000
@@ -1,6 +1,7 @@
-@comment $NetBSD: PLIST,v 1.2 2020/07/27 00:29:04 bacon Exp $
+@comment $NetBSD: PLIST,v 1.3 2021/03/20 18:17:07 bacon Exp $
 bin/bcftools
 bin/color-chrs
+bin/gff2gff.py
 bin/guess-ploidy
 bin/plot-roh
 bin/plot-vcfstats
@@ -34,12 +35,13 @@
 libexec/bcftools/parental-origin.so
 libexec/bcftools/prune.so
 libexec/bcftools/remove-overlaps.so
+libexec/bcftools/scatter.so
 libexec/bcftools/setGT.so
 libexec/bcftools/smpl-stats.so
 libexec/bcftools/split-vep.so
 libexec/bcftools/split.so
 libexec/bcftools/tag2tag.so
-libexec/bcftools/trio-dnm.so
+libexec/bcftools/trio-dnm2.so
 libexec/bcftools/trio-stats.so
 libexec/bcftools/trio-switch-rate.so
 libexec/bcftools/variantkey-hex.so
diff -r c60e89e20eb4 -r 523f46b9982b biology/bcftools/distinfo
--- a/biology/bcftools/distinfo Sat Mar 20 15:49:07 2021 +0000
+++ b/biology/bcftools/distinfo Sat Mar 20 18:17:07 2021 +0000
@@ -1,8 +1,7 @@
-$NetBSD: distinfo,v 1.2 2020/07/27 00:29:04 bacon Exp $
+$NetBSD: distinfo,v 1.3 2021/03/20 18:17:07 bacon Exp $
 
-SHA1 (bcftools-1.10.2.tar.gz) = b19c9ba06b1c8e8f135c1e0ab0e4ff713a291bf4
-RMD160 (bcftools-1.10.2.tar.gz) = 7713e8c5bd4195eb610544adb26158c16525fdac
-SHA512 (bcftools-1.10.2.tar.gz) = 12c004603db557ac69098e83ad3aaa5762b02b4718b79f3dc259fbcc5c74b8dad3726b5f61efb57f0b8e3d0349577f7934240f36c82bd98849885a5593791995
-Size (bcftools-1.10.2.tar.gz) = 2880994 bytes
-SHA1 (patch-Makefile) = 1f1397e9b0389a7b4fccc9eae87981e7ce1d7980
-SHA1 (patch-misc_run-roh.pl) = 8a29ee7b1001af6670955f174ce4dbab31f05659
+SHA1 (bcftools-1.12.tar.gz) = 17ded5a60da7a42d18fef5a846791ed295f69622
+RMD160 (bcftools-1.12.tar.gz) = 9d3a16c8266bcdd8f2a10f099aec3fc19da82a98
+SHA512 (bcftools-1.12.tar.gz) = f43074989a01cf4ef32a968935f5e5f3eacf2c04b9aa558d739166e3d96d3a498965d27db6482b2992b5d60fed3d2945ef3fd61fcc79b5dbe062994d49df4ad2
+Size (bcftools-1.12.tar.gz) = 3048508 bytes
+SHA1 (patch-Makefile) = 9dfe7b5dcf77deac6d248d7612440780ec8a3731
diff -r c60e89e20eb4 -r 523f46b9982b biology/bcftools/patches/patch-Makefile
--- a/biology/bcftools/patches/patch-Makefile   Sat Mar 20 15:49:07 2021 +0000
+++ b/biology/bcftools/patches/patch-Makefile   Sat Mar 20 18:17:07 2021 +0000
@@ -1,49 +1,13 @@
-$NetBSD: patch-Makefile,v 1.1 2020/07/27 00:29:04 bacon Exp $
+$NetBSD: patch-Makefile,v 1.2 2021/03/20 18:17:07 bacon Exp $
 
 # Respect pkgsrc env
 
---- Makefile.orig      2019-12-19 09:57:32.000000000 +0000
+--- Makefile.orig      2021-03-19 17:42:33.842623449 +0000
 +++ Makefile
-@@ -22,12 +22,12 @@
- # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
- # DEALINGS IN THE SOFTWARE.
- 
--CC       = gcc
--AR       = ar
--RANLIB   = ranlib
--CPPFLAGS =
--CFLAGS   = -g -Wall -O2
--LDFLAGS  =
-+CC       ?= gcc
-+AR       ?= ar
-+RANLIB   ?= ranlib
-+# CPPFLAGS =
-+CFLAGS   ?= -g -Wall -O2
-+# LDFLAGS  =
- LIBS     =
- 
- DYNAMIC_FLAGS = -rdynamic
-@@ -45,12 +45,12 @@ OBJS     = main.o vcfindex.o tabix.o \
-            ccall.o em.o prob1.o kmin.o # the original samtools calling
- PLUGIN_OBJS = vcfplugin.o
- 
--prefix      = /usr/local
--exec_prefix = $(prefix)
-+PREFIX      ?= /usr/local
-+exec_prefix = $(PREFIX)
- bindir      = $(exec_prefix)/bin
- libdir      = $(exec_prefix)/lib
- libexecdir  = $(exec_prefix)/libexec
--mandir      = $(prefix)/share/man
-+mandir      = $(PREFIX)/share/man
- man1dir     = $(mandir)/man1
- # Installation location for $(PLUGINS)
- plugindir   = $(libexecdir)/bcftools
-@@ -59,12 +59,11 @@ pluginpath  = $(plugindir)
- misc_bindir = $(bindir)
+@@ -60,11 +60,11 @@ misc_bindir = $(bindir)
  
  MKDIR_P = mkdir -p
--INSTALL = install -p
+ INSTALL = install -p
 -INSTALL_DATA    = $(INSTALL) -m 644
 -INSTALL_DIR     = $(MKDIR_P) -m 755
 -INSTALL_MAN     = $(INSTALL_DATA)
@@ -57,12 +21,3 @@
  
  PROGRAMS = bcftools
  MISC_SCRIPTS = \
-@@ -78,7 +77,7 @@ TEST_PROGRAMS = test/test-rbuf test/test
- 
- ALL_CPPFLAGS = -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS)
- ALL_LDFLAGS  = $(HTSLIB_LDFLAGS) $(LDFLAGS)
--ALL_LIBS     = -lz $(DL_LIBS) $(LIBS)
-+ALL_LIBS     = -lz $(LIBS)
- 
- all: $(PROGRAMS) $(TEST_PROGRAMS) plugins
- 
diff -r c60e89e20eb4 -r 523f46b9982b biology/bcftools/patches/patch-misc_run-roh.pl
--- a/biology/bcftools/patches/patch-misc_run-roh.pl    Sat Mar 20 15:49:07 2021 +0000
+++ /dev/null   Thu Jan 01 00:00:00 1970 +0000
@@ -1,24 +0,0 @@
-$NetBSD: patch-misc_run-roh.pl,v 1.1 2020/07/27 00:29:04 bacon Exp $
-
-# bash path
-
---- misc/run-roh.pl.orig       2019-12-19 09:57:32.000000000 +0000
-+++ misc/run-roh.pl
-@@ -110,7 +110,7 @@ sub cmd
- 
-     if ( $args{verbose} ) { print STDERR $cmd,"\n"; }
- 
--    # Why not to use backticks? Perl calls /bin/sh, which is often bash. To get the correct
-+    # Why not to use backticks? Perl calls bash, which is often bash. To get the correct
-     #   status of failing pipes, it must be called with the pipefail option.
- 
-     my $kid_io;
-@@ -127,7 +127,7 @@ sub cmd
-     else 
-     {      
-         # child
--        exec('/bin/bash', '-o','pipefail','-c', $cmd) or error("Failed to run the command [/bin/sh -o pipefail -c $cmd]: $!");
-+        exec('bash', '-c', $cmd) or error("Failed to run the command [bash -c $cmd]: $!");
-     }
- 
-     if ( exists($args{exit_on_error}) && !$args{exit_on_error} ) { return @out; }
diff -r c60e89e20eb4 -r 523f46b9982b biology/htslib/Makefile
--- a/biology/htslib/Makefile   Sat Mar 20 15:49:07 2021 +0000
+++ b/biology/htslib/Makefile   Sat Mar 20 18:17:07 2021 +0000
@@ -1,9 +1,10 @@
-# $NetBSD: Makefile,v 1.18 2020/08/31 18:06:39 wiz Exp $
+# $NetBSD: Makefile,v 1.19 2021/03/20 18:17:07 bacon Exp $
 
-DISTNAME=      htslib-1.10.2
-PKGREVISION=   2
+DISTNAME=      htslib-1.12
 CATEGORIES=    biology
-MASTER_SITES=  ${MASTER_SITE_GITHUB:=samtools/}
+# Github-generated distfiles are incomplete, use custom tarballs instead
+MASTER_SITES=  https://github.com/samtools/htslib/releases/download/${PKGVERSION_NOREV}/
+EXTRACT_SUFX=  .tar.bz2
 
 MAINTAINER=    bacon%NetBSD.org@localhost
 HOMEPAGE=      https://www.htslib.org/
@@ -23,6 +24,7 @@
 CONFIGURE_ARGS+=       --enable-libcurl
 PKGCONFIG_OVERRIDE=    htslib.pc.in
 TEST_TARGET=           test
+MAKE_ENV+=             BUILT_TEST_PROGRAMS=''
 
 pre-configure:
        cd ${WRKSRC} && autoreconf -if
diff -r c60e89e20eb4 -r 523f46b9982b biology/htslib/PLIST
--- a/biology/htslib/PLIST      Sat Mar 20 15:49:07 2021 +0000
+++ b/biology/htslib/PLIST      Sat Mar 20 18:17:07 2021 +0000
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.2 2020/07/22 14:50:14 bacon Exp $
+@comment $NetBSD: PLIST,v 1.3 2021/03/20 18:17:07 bacon Exp $
 bin/bgzip
 bin/htsfile
 bin/tabix
@@ -9,6 +9,7 @@
 include/htslib/hts.h
 include/htslib/hts_defs.h
 include/htslib/hts_endian.h
+include/htslib/hts_expr.h
 include/htslib/hts_log.h
 include/htslib/hts_os.h
 include/htslib/kbitset.h
@@ -17,6 +18,7 @@
 include/htslib/khash_str2int.h
 include/htslib/klist.h
 include/htslib/knetfile.h
+include/htslib/kroundup.h
 include/htslib/kseq.h
 include/htslib/ksort.h
 include/htslib/kstring.h
diff -r c60e89e20eb4 -r 523f46b9982b biology/htslib/buildlink3.mk
--- a/biology/htslib/buildlink3.mk      Sat Mar 20 15:49:07 2021 +0000
+++ b/biology/htslib/buildlink3.mk      Sat Mar 20 18:17:07 2021 +0000
@@ -1,11 +1,11 @@
-# $NetBSD: buildlink3.mk,v 1.4 2020/07/22 15:36:55 bacon Exp $
+# $NetBSD: buildlink3.mk,v 1.5 2021/03/20 18:17:07 bacon Exp $
 
 BUILDLINK_TREE+=       htslib
 
 .if !defined(HTSLIB_BUILDLINK3_MK)
 HTSLIB_BUILDLINK3_MK:=
 
-BUILDLINK_API_DEPENDS.htslib+= htslib>=1.8
+BUILDLINK_API_DEPENDS.htslib+= htslib>=1.10.2
 BUILDLINK_ABI_DEPENDS.htslib+= htslib>=1.10.2
 BUILDLINK_PKGSRCDIR.htslib?=   ../../biology/htslib
 
diff -r c60e89e20eb4 -r 523f46b9982b biology/htslib/distinfo
--- a/biology/htslib/distinfo   Sat Mar 20 15:49:07 2021 +0000
+++ b/biology/htslib/distinfo   Sat Mar 20 18:17:07 2021 +0000
@@ -1,9 +1,6 @@
-$NetBSD: distinfo,v 1.3 2020/07/22 14:50:14 bacon Exp $
+$NetBSD: distinfo,v 1.4 2021/03/20 18:17:07 bacon Exp $
 
-SHA1 (htslib-1.10.2.tar.gz) = 0ac4b86e49556d7dcaa89d4cce2661c9ca706631
-RMD160 (htslib-1.10.2.tar.gz) = 6d8b6a362297345420dc9acc544029276ce4b1b6
-SHA512 (htslib-1.10.2.tar.gz) = 7a91c15ca1de35653d068dc57ae511ad791ae0bd8504867d4e60c46e813e58b441409541197cde3b2a37840e60331336aebc627ecbf5c64fca1af63dd05f8f9e
-Size (htslib-1.10.2.tar.gz) = 1452177 bytes
-SHA1 (patch-Makefile) = e13333dd97ecd6c6753d14c1b738d6e5934a2911
-SHA1 (patch-cram_open__trace__file.c) = 49b47e13786317e652a8ec810cc91f10d21bb8ea
-SHA1 (patch-hfile__libcurl.c) = 2a143818f1099ef01c57a3c904060a76abb63f14
+SHA1 (htslib-1.12.tar.bz2) = 8cab518f97bbdf43165320c3a4bdef1e9a42893a
+RMD160 (htslib-1.12.tar.bz2) = 3d93d91db8c382f42b8ad0843609cabd3b502b46
+SHA512 (htslib-1.12.tar.bz2) = a810c646561f5c8b3a19b73ac22ec5f25b04d4e88e1314988881a8120c54106591d1d65aa708bbe2608f0065ca8abe92bdd70ef59a0dd0cdf63ff45c10957092
+Size (htslib-1.12.tar.bz2) = 4094458 bytes
diff -r c60e89e20eb4 -r 523f46b9982b biology/htslib/patches/patch-Makefile
--- a/biology/htslib/patches/patch-Makefile     Sat Mar 20 15:49:07 2021 +0000
+++ /dev/null   Thu Jan 01 00:00:00 1970 +0000
@@ -1,76 +0,0 @@
-$NetBSD: patch-Makefile,v 1.1 2020/07/22 14:50:14 bacon Exp $
-
-# Respect pkgsrc env
-
---- Makefile.orig      2019-12-19 09:54:30.000000000 +0000
-+++ Makefile
-@@ -22,44 +22,43 @@
- # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
- # DEALINGS IN THE SOFTWARE.
- 
--CC     = gcc
--AR     = ar
--RANLIB = ranlib
-+CC     ?= gcc
-+AR     ?= ar
-+RANLIB ?= ranlib
- 
- # Default libraries to link if configure is not used
- htslib_default_libs = -lz -lm -lbz2 -llzma -lcurl
- 
--CPPFLAGS =
-+# CPPFLAGS =
- # TODO: make the 64-bit support for VCF optional via configure, for now add -DVCF_ALLOW_INT64
- #       to CFLAGS manually, here or in config.mk if the latter exists.
- # TODO: probably update cram code to make it compile cleanly with -Wc++-compat
- # For testing strict C99 support add -std=c99 -D_XOPEN_SOURCE=600
- #CFLAGS   = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600
--CFLAGS   = -g -Wall -O2 -fvisibility=hidden
-+CFLAGS   ?= -g -Wall -O2 -fvisibility=hidden
- EXTRA_CFLAGS_PIC = -fpic
--LDFLAGS  = -fvisibility=hidden
-+LDFLAGS  ?= -fvisibility=hidden
- LIBS     = $(htslib_default_libs)
- 
--prefix      = /usr/local
--exec_prefix = $(prefix)
-+PREFIX      ?= /usr/local
-+exec_prefix = $(PREFIX)
- bindir      = $(exec_prefix)/bin
--includedir  = $(prefix)/include
-+includedir  = $(PREFIX)/include
- libdir      = $(exec_prefix)/lib
- libexecdir  = $(exec_prefix)/libexec
--datarootdir = $(prefix)/share
-+datarootdir = $(PREFIX)/share
- mandir      = $(datarootdir)/man
- man1dir     = $(mandir)/man1
- man5dir     = $(mandir)/man5
- man7dir     = $(mandir)/man7
- pkgconfigdir= $(libdir)/pkgconfig
- 
--MKDIR_P = mkdir -p
--INSTALL = install -p
--INSTALL_DATA    = $(INSTALL) -m 644



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