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, 13 insertions, 56 deletions

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