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

17 files changed, 32 insertions, 148 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
diff --git a/biology/htslib/Makefile b/biology/htslib/Makefile
index 733ec0c41dea..17779dfd3503 100644
--- a/biology/htslib/Makefile
+++ b/biology/htslib/Makefile
@@ -2,8 +2,10 @@
 # $FreeBSD$
 
 PORTNAME=	htslib
-DISTVERSION=	1.11.0
+DISTVERSION=	1.12
 CATEGORIES=	biology devel
+# Github generated distfiles are incomplete, so use custom tarball
+MASTER_SITES=	https://github.com/samtools/htslib/releases/download/${DISTVERSION}/
 
 MAINTAINER=	jwb@FreeBSD.org
 COMMENT=	C library for high-throughput sequencing data formats
@@ -15,12 +17,10 @@ LICENSE_FILE=	${WRKSRC}/LICENSE
 LIB_DEPENDS=	libdeflate.so:archivers/libdeflate
 TEST_DEPENDS=	bash:shells/bash
 
-USES=		autoreconf gmake localbase pathfix perl5 shebangfix
-USE_GITHUB=	yes
+USES=		autoreconf gmake localbase pathfix perl5 shebangfix tar:bzip2
 USE_PERL5=	test
 USE_LDCONFIG=	yes
 
-GH_ACCOUNT=		samtools
 GNU_CONFIGURE=		yes
 PATHFIX_MAKEFILEIN=	Makefile
 SHEBANG_FILES=		test/*.pl
diff --git a/biology/htslib/distinfo b/biology/htslib/distinfo
index ef59ac4df246..2bc449b5deb6 100644
--- a/biology/htslib/distinfo
+++ b/biology/htslib/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1602982298
-SHA256 (samtools-htslib-1.11.0_GH0.tar.gz) = 55356e78f25a20194488d94308335f409c3757101398961388caf38d3cce12dd
-SIZE (samtools-htslib-1.11.0_GH0.tar.gz) = 1485848
+TIMESTAMP = 1616112272
+SHA256 (htslib-1.12.tar.bz2) = 2280141b46e953ba4ae01b98335a84f8e6ccbdb6d5cdbab7f70ee4f7e3b6f4ca
+SIZE (htslib-1.12.tar.bz2) = 4094458
diff --git a/biology/htslib/files/patch-Makefile b/biology/htslib/files/patch-Makefile
index 6f8216bbc7bb..7f91465d2ccd 100644
--- a/biology/htslib/files/patch-Makefile
+++ b/biology/htslib/files/patch-Makefile
@@ -1,16 +1,6 @@
---- Makefile.orig	2020-10-18 00:44:56 UTC
+--- Makefile.orig	2021-03-20 15:53:14 UTC
 +++ Makefile
-@@ -40,7 +40,8 @@ EXTRA_CFLAGS_PIC = -fpic
- LDFLAGS  = -fvisibility=hidden
- LIBS     = $(htslib_default_libs)
- 
--prefix      = /usr/local
-+PREFIX      ?= /usr/local
-+prefix      = $(PREFIX)
- exec_prefix = $(prefix)
- bindir      = $(exec_prefix)/bin
- includedir  = $(prefix)/include
-@@ -53,13 +54,14 @@ man5dir     = $(mandir)/man5
+@@ -53,13 +53,14 @@ man5dir     = $(mandir)/man5
  man7dir     = $(mandir)/man7
  pkgconfigdir= $(prefix)/libdata/pkgconfig
  
@@ -32,7 +22,7 @@
  
  # Set by config.mk if plugins are enabled
  plugindir =
-@@ -100,7 +102,7 @@ BUILT_THRASH_PROGRAMS = \
+@@ -102,7 +103,7 @@ BUILT_THRASH_PROGRAMS = \
  	test/thrash_threads6 \
  	test/thrash_threads7
  
@@ -40,4 +30,4 @@
 +all: lib-static lib-shared $(BUILT_PROGRAMS) plugins \
       htslib_static.mk htslib-uninstalled.pc
  
- HTSPREFIX =
+ ALL_CPPFLAGS = -I. $(CPPFLAGS)
diff --git a/biology/htslib/files/patch-hfile__libcurl.c b/biology/htslib/files/patch-hfile__libcurl.c
deleted file mode 100644
index 2406056b1c04..000000000000
--- a/biology/htslib/files/patch-hfile__libcurl.c
+++ /dev/null
@@ -1,24 +0,0 @@
---- hfile_libcurl.c.orig	2020-09-22 12:15:49 UTC
-+++ hfile_libcurl.c
-@@ -22,6 +22,10 @@ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR O
- FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
- DEALINGS IN THE SOFTWARE.  */
- 
-+#ifndef ENOTRECOVERABLE
-+#define ENOTRECOVERABLE EIO
-+#endif
-+
- #define HTS_BUILDING_LIBRARY // Enables HTSLIB_EXPORT, see htslib/hts_defs.h
- #include <config.h>
- 
-@@ -73,6 +77,10 @@ typedef struct {
-     unsigned int num;
-     unsigned int size;
- } hdrlist;
-+
-+#ifndef ENOTRECOVERABLE
-+#define ENOTRECOVERABLE EIO
-+#endif
- 
- typedef struct {
-     hdrlist fixed;                   // List of headers supplied at hopen()
diff --git a/biology/htslib/files/patch-sam.c b/biology/htslib/files/patch-sam.c
deleted file mode 100644
index 679b4d71967d..000000000000
--- a/biology/htslib/files/patch-sam.c
+++ /dev/null
@@ -1,10 +0,0 @@
---- sam.c.orig	2020-10-18 00:50:46 UTC
-+++ sam.c
-@@ -35,6 +35,7 @@ DEALINGS IN THE SOFTWARE.  */
- #include <assert.h>
- #include <signal.h>
- #include <inttypes.h>
-+#include <unistd.h>	// usleep()
- 
- // Suppress deprecation message for cigar_tab, which we initialise
- #include "htslib/hts_defs.h"
diff --git a/biology/htslib/pkg-plist b/biology/htslib/pkg-plist
index 06e7972133d5..e2ebe3a2e8d6 100644
--- a/biology/htslib/pkg-plist
+++ b/biology/htslib/pkg-plist
@@ -8,6 +8,7 @@ include/htslib/hfile.h
 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
@@ -30,7 +31,7 @@ include/htslib/vcf_sweep.h
 include/htslib/vcfutils.h
 lib/libhts.a
 lib/libhts.so
-lib/libhts.so.1.11
+lib/libhts.so.%%PORTVERSION%%
 lib/libhts.so.3
 libdata/pkgconfig/htslib.pc
 man/man1/bgzip.1.gz
diff --git a/biology/samtools/Makefile b/biology/samtools/Makefile
index 74b6236a030a..55bfe3dd5c12 100644
--- a/biology/samtools/Makefile
+++ b/biology/samtools/Makefile
@@ -2,7 +2,7 @@
 # $FreeBSD$
 
 PORTNAME=	samtools
-DISTVERSION=	1.11
+DISTVERSION=	1.12
 CATEGORIES=	biology
 
 MAINTAINER=	jwb@FreeBSD.org
@@ -11,7 +11,7 @@ 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
 
 USES=		autoreconf gmake localbase ncurses perl5 python:env shebangfix
diff --git a/biology/samtools/distinfo b/biology/samtools/distinfo
index d0c046e7d011..08b69e957221 100644
--- a/biology/samtools/distinfo
+++ b/biology/samtools/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1602982679
-SHA256 (samtools-samtools-1.11_GH0.tar.gz) = 80a54e93c5d111c15c005ee96a578bcd7e1bde34dba2242d981c539ff32f1738
-SIZE (samtools-samtools-1.11_GH0.tar.gz) = 4516328
+TIMESTAMP = 1616112844
+SHA256 (samtools-samtools-1.12_GH0.tar.gz) = a31695aca88b6acf52e1b579d84edb6b54f7b1b22227aad1ef6c6ccdd10314cf
+SIZE (samtools-samtools-1.12_GH0.tar.gz) = 4528460
diff --git a/biology/samtools/files/patch-Makefile b/biology/samtools/files/patch-Makefile
index 3a175dd2115b..de890df5e224 100644
--- a/biology/samtools/files/patch-Makefile
+++ b/biology/samtools/files/patch-Makefile
@@ -1,16 +1,6 @@
---- Makefile.orig	2020-10-18 00:55:50 UTC
+--- Makefile.orig	2021-03-17 09:14:26 UTC
 +++ Makefile
-@@ -49,7 +49,8 @@ AOBJS=      bam_index.o bam_plcmd.o sam_view.o bam_fas
- 	    bam_ampliconclip.o amplicon_stats.o
- LZ4OBJS  =  $(LZ4DIR)/lz4.o
- 
--prefix      = /usr/local
-+PREFIX      ?= /usr/local
-+prefix      = $(PREFIX)
- exec_prefix = $(prefix)
- bindir      = $(exec_prefix)/bin
- datarootdir = $(prefix)/share
-@@ -59,14 +60,14 @@ man1dir     = $(mandir)/man1
+@@ -59,14 +59,14 @@ man1dir     = $(mandir)/man1
  # Installation location for $(MISC_PROGRAMS) and $(MISC_SCRIPTS)
  misc_bindir = $(bindir)
  
@@ -23,8 +13,8 @@
 -INSTALL_SCRIPT  = $(INSTALL_PROGRAM)
 -
 +# Use BSD_INSTALL_PROGRAM to strip when WITH_DEBUG not set
-+MKDIR_P 	= mkdir -p
-+INSTALL 	= install -p
++MKDIR_P         = mkdir -p
++INSTALL         = install -p
 +INSTALL_DATA    = ${BSD_INSTALL_DATA}
 +INSTALL_DIR     = $(MKDIR_P)
 +INSTALL_MAN     = ${BSD_INSTALL_MAN}
diff --git a/biology/samtools/files/patch-test_test.pl b/biology/samtools/files/patch-test_test.pl
deleted file mode 100644
index 8800086e39b0..000000000000
--- a/biology/samtools/files/patch-test_test.pl
+++ /dev/null
@@ -1,20 +0,0 @@
---- test/test.pl.orig	2020-07-21 20:48:50 UTC
-+++ test/test.pl
-@@ -907,7 +907,7 @@ sub test_usage
-     my $command = $args{cmd};
-     my $commandpath = $$opts{bin}."/".$command;
-     my ($ret,$out,$err) = _cmd("$commandpath $args{redirection}");
--    if ( $err =~ m/\/bin\/bash.*no.*such/i ) { failed($opts,msg=>$test,reason=>"could not run $commandpath: $out"); return; }
-+    if ( $err =~ m/bash.*no.*such/i ) { failed($opts,msg=>$test,reason=>"could not run $commandpath: $out"); return; }
- 
-     my @sections = ($err =~ m/(^[A-Za-z]+.*?)(?:(?=^[A-Za-z]+:)|\z)/msg);
- 
-@@ -965,7 +965,7 @@ sub test_usage_subcommand
-     my $commandpath = $$opts{bin}."/".$command;
-     my ($ret,$out,$err) = _cmd("$commandpath $subcommand $args{redirection}");
- 
--    if ( $err =~ m/\/bin\/bash.*no.*such/i ) { failed($opts,msg=>$test,reason=>"could not run $commandpath $subcommand: $out"); return; }
-+    if ( $err =~ m/bash.*no.*such/i ) { failed($opts,msg=>$test,reason=>"could not run $commandpath $subcommand: $out"); return; }
- 
-     if ( $err =~ m/not.*implemented/is ) { failed($opts,msg=>$test,reason=>"subcommand indicates it is not implemented",expect_fail=>1); return; }
- 
diff --git a/biology/samtools/pkg-plist b/biology/samtools/pkg-plist
index 4c35d4bb0e69..19b73d4ab8e7 100644
--- a/biology/samtools/pkg-plist
+++ b/biology/samtools/pkg-plist
@@ -2,6 +2,7 @@ bin/ace2sam
 bin/blast2sam.pl
 bin/bowtie2sam.pl
 bin/export2sam.pl
+bin/fasta-sanitize.pl
 bin/interpolate_sam.pl
 bin/maq2sam-long
 bin/maq2sam-short