bcftools: Update to 1.12

To: pkgsrc-wip-changes%NetBSD.org@localhost
Subject: bcftools: Update to 1.12
From: Jason Bacon <bacon%NetBSD.org@localhost>
Date: Fri, 19 Mar 2021 17:47:42 +0000
Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Fri Mar 19 12:47:42 2021 -0500
Changeset:	891d08e1943d6898eea1d1fd4db11cddcfb5b30e

Modified Files:
	bcftools/Makefile
	bcftools/PLIST
	bcftools/distinfo
	bcftools/patches/patch-Makefile
Removed Files:
	bcftools/patches/patch-misc_run-roh.pl

Log Message:
bcftools: Update to 1.12

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=891d08e1943d6898eea1d1fd4db11cddcfb5b30e

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 bcftools/Makefile                      |  2 +-
 bcftools/PLIST                         |  4 ++-
 bcftools/distinfo                      | 11 ++++----
 bcftools/patches/patch-Makefile        | 51 ++--------------------------------
 bcftools/patches/patch-misc_run-roh.pl | 24 ----------------
 5 files changed, 12 insertions(+), 80 deletions(-)

diffs:
diff --git a/bcftools/Makefile b/bcftools/Makefile
index 2efe84b939..3bd615c712 100644
--- a/bcftools/Makefile
+++ b/bcftools/Makefile
@@ -1,6 +1,6 @@
 # $NetBSD$
 
-DISTNAME=	bcftools-1.10.2
+DISTNAME=	bcftools-1.12
 CATEGORIES=	biology
 MASTER_SITES=	${MASTER_SITE_GITHUB:=samtools/}
 
diff --git a/bcftools/PLIST b/bcftools/PLIST
index d0a6ac2119..ebe003576a 100644
--- a/bcftools/PLIST
+++ b/bcftools/PLIST
@@ -1,6 +1,7 @@
 @comment $NetBSD$
 bin/bcftools
 bin/color-chrs
+bin/gff2gff.py
 bin/guess-ploidy
 bin/plot-roh
 bin/plot-vcfstats
@@ -34,12 +35,13 @@ libexec/bcftools/missing2ref.so
 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 --git a/bcftools/distinfo b/bcftools/distinfo
index fcd6846ef3..ef1b4c3540 100644
--- a/bcftools/distinfo
+++ b/bcftools/distinfo
@@ -1,8 +1,7 @@
 $NetBSD$
 
-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 --git a/bcftools/patches/patch-Makefile b/bcftools/patches/patch-Makefile
index 95228d8f42..eaaabf29e9 100644
--- a/bcftools/patches/patch-Makefile
+++ b/bcftools/patches/patch-Makefile
@@ -2,48 +2,12 @@ $NetBSD$
 
 # 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 @@ $NetBSD$
  
  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) $(TEST_PROGRAMS) plugins
- 
diff --git a/bcftools/patches/patch-misc_run-roh.pl b/bcftools/patches/patch-misc_run-roh.pl
deleted file mode 100644
index a441e19f69..0000000000
--- a/bcftools/patches/patch-misc_run-roh.pl
+++ /dev/null
@@ -1,24 +0,0 @@
-$NetBSD$
-
-# 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; }
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