biology/htslib: Update to 1.12

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

Numerous enhancements, performance improvements, and bug fixes since 1.11

Build-tested all other htslib dependents, no revbumps should be needed

Reported by:    portscout

6 files changed, 9 insertions, 53 deletions

diff --git a/biology/bcftools/Makefile b/biology/bcftools/Makefile
index 964affb3cd6f..f70a8d828a2d 100644
--- a/biology/bcftools/Makefile
+++ b/biology/bcftools/Makefile
@@ -2,7 +2,7 @@
 # $FreeBSD$
 
 PORTNAME=	bcftools
-PORTVERSION=	1.11
+PORTVERSION=	1.12
 CATEGORIES=	biology
 
 MAINTAINER=	jwb@FreeBSD.org
@@ -11,14 +11,13 @@ COMMENT=	Tools for manipulating next-generation sequencing data
 LICENSE=	MIT
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
-LIB_DEPENDS=	libhts.so.3:biology/htslib
+LIB_DEPENDS=	libhts.so:biology/htslib
 TEST_DEPENDS=	bash:shells/bash
 RUN_DEPENDS=	bash:shells/bash
 
 USES=		autoreconf gmake localbase perl5 python:env shebangfix
 
 USE_GITHUB=	yes
-USE_LDCONFIG=	${PREFIX}/libexec/${PORTNAME}
 USE_PERL5=	test
 
 GH_ACCOUNT=	samtools
diff --git a/biology/bcftools/distinfo b/biology/bcftools/distinfo
index aac1660e88f1..204108d9af60 100644
--- a/biology/bcftools/distinfo
+++ b/biology/bcftools/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1603028344
-SHA256 (samtools-bcftools-1.11_GH0.tar.gz) = f2d9a09fd7920754b60948b81ec047882864213b93a0cd1ef0372b0e025cba3f
-SIZE (samtools-bcftools-1.11_GH0.tar.gz) = 3004923
+TIMESTAMP = 1616112968
+SHA256 (samtools-bcftools-1.12_GH0.tar.gz) = b29e6d41ca0bb3f1761bee81be0c423329928a724a75501641c1ac5065d65526
+SIZE (samtools-bcftools-1.12_GH0.tar.gz) = 3048508
diff --git a/biology/bcftools/files/patch-Makefile b/biology/bcftools/files/patch-Makefile
index 8dc6a8e96e69..3299954ae45b 100644
--- a/biology/bcftools/files/patch-Makefile
+++ b/biology/bcftools/files/patch-Makefile
@@ -1,16 +1,6 @@
---- Makefile.orig	2020-10-18 13:31:52 UTC
+--- Makefile.orig	2021-03-17 09:16:18 UTC
 +++ Makefile
-@@ -45,7 +45,8 @@ 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
-+PREFIX      ?= /usr/local
-+prefix      = $(PREFIX)
- exec_prefix = $(prefix)
- bindir      = $(exec_prefix)/bin
- libdir      = $(exec_prefix)/lib
-@@ -58,13 +59,14 @@ pluginpath  = $(plugindir)
+@@ -58,13 +58,14 @@ pluginpath  = $(plugindir)
  # Installation location for $(MISC_PROGRAMS) and $(MISC_SCRIPTS)
  misc_bindir = $(bindir)
  
@@ -32,7 +22,7 @@
  
  PROGRAMS = bcftools
  MISC_SCRIPTS = \
-@@ -142,7 +144,7 @@ print-version:
+@@ -142,7 +143,7 @@ print-version:
  ifdef USE_GPL
      main.o : EXTRA_CPPFLAGS += -DUSE_GPL
      OBJS += polysomy.o peakfit.o
diff --git a/biology/bcftools/files/patch-test_test.pl b/biology/bcftools/files/patch-test_test.pl
deleted file mode 100644
index 39ccb4466b54..000000000000
--- a/biology/bcftools/files/patch-test_test.pl
+++ /dev/null
@@ -1,20 +0,0 @@
---- test/test.pl.orig	2020-10-18 13:36:42 UTC
-+++ test/test.pl
-@@ -1236,7 +1236,7 @@ sub test_usage
-     my $command = $args{cmd};
-     my $commandpath = $$opts{bin}."/".$command;
-     my ($ret,$out) = _cmd("$commandpath $args{redirection} 2>&1");
--    if ( $out =~ m/\/bin\/bash.*no.*such/i ) { failed($opts,$test,"could not run $commandpath: $out"); return; }
-+    if ( $out =~ m/bash.*no.*such/i ) { failed($opts,$test,"could not run $commandpath: $out"); return; }
- 
-     my @sections = ($out =~ m/(^[A-Za-z]+.*?)(?:(?=^[A-Za-z]+:)|\z)/msg);
- 
-@@ -1291,7 +1291,7 @@ sub test_usage_subcommand
-     my $subcommand = $args{subcmd};
-     my $commandpath = $$opts{bin}."/".$command;
-     my ($ret,$out) = _cmd("$commandpath $subcommand $args{redirection} 2>&1");
--    if ( $out =~ m/\/bin\/bash.*no.*such/i ) { failed($opts,$test,"could not run $commandpath $subcommand: $out"); return; }
-+    if ( $out =~ m/bash.*no.*such/i ) { failed($opts,$test,"could not run $commandpath $subcommand: $out"); return; }
- 
-     my @sections = ($out =~ m/(^[A-Za-z]+.*?)(?:(?=^[A-Za-z]+:)|\z)/msg);
- 
diff --git a/biology/bcftools/files/pkg-message.in b/biology/bcftools/files/pkg-message.in
deleted file mode 100644
index 8bee64d8ea83..000000000000
--- a/biology/bcftools/files/pkg-message.in
+++ /dev/null
@@ -1,13 +0,0 @@
-[
-{ type: install
-  message: <<EOM
-The miscellaneous tools included with Bcftools have been installed to
-%%PREFIX%%/bin/samtools_misc
-
-Add that directory to your path if you want to use these tools.
-
-Some of these tools depend on Perl5/Python, and it will need to be installed to
-use them.
-EOM
-}
-]
diff --git a/biology/bcftools/pkg-plist b/biology/bcftools/pkg-plist
index ed393533217b..11f94eafff86 100644
--- a/biology/bcftools/pkg-plist
+++ b/biology/bcftools/pkg-plist
@@ -40,7 +40,7 @@ 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