htslib: Update to 1.12

[Jason Bacon <bacon%NetBSD.org@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Fri Mar 19 12:15:06 2021 -0500
Changeset:	01edf6f17a1fbde9459cba6ca2efd7b06ca77857

Modified Files:
	htslib/Makefile
	htslib/PLIST
	htslib/distinfo
Removed Files:
	htslib/patches/patch-Makefile

Log Message:
htslib: 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=01edf6f17a1fbde9459cba6ca2efd7b06ca77857

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

diffstat:
 htslib/Makefile               |  6 +++--
 htslib/PLIST                  |  3 ++-
 htslib/distinfo               |  9 +++----
 htslib/patches/patch-Makefile | 58 -------------------------------------------
 4 files changed, 10 insertions(+), 66 deletions(-)

diffs:
diff --git a/htslib/Makefile b/htslib/Makefile
index 03ac16a9c9..57395c0fd2 100644
--- a/htslib/Makefile
+++ b/htslib/Makefile
@@ -1,8 +1,10 @@
 # $NetBSD$
 
-DISTNAME=	htslib-1.11.0
+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/
diff --git a/htslib/PLIST b/htslib/PLIST
index fdf49ff8f4..d57416fbdf 100644
--- a/htslib/PLIST
+++ b/htslib/PLIST
@@ -9,6 +9,7 @@ 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
@@ -31,7 +32,7 @@ include/htslib/vcf_sweep.h
 include/htslib/vcfutils.h
 lib/libhts.a
 lib/libhts.so
-lib/libhts.so.1.11
+lib/libhts.so.${PKGVERSION}
 lib/libhts.so.3
 lib/pkgconfig/htslib.pc
 man/man1/bgzip.1
diff --git a/htslib/distinfo b/htslib/distinfo
index a160e4c0ae..00774a52d3 100644
--- a/htslib/distinfo
+++ b/htslib/distinfo
@@ -1,7 +1,6 @@
 $NetBSD$
 
-SHA1 (htslib-1.11.0.tar.gz) = 8ecf722ae5988f44667b22057ba17d4c2223408e
-RMD160 (htslib-1.11.0.tar.gz) = e7c388dbc6b4a9a89e107c1b319e02c95717be41
-SHA512 (htslib-1.11.0.tar.gz) = 146468f25fcc7781a8f4528af8f9823d16e22f6b1e87c5d29bd3e8d323c9bc403a57b6344ddfb569629be71f04e710af56cfb7d876dc7ed7cce73e05f71624a3
-Size (htslib-1.11.0.tar.gz) = 1485848 bytes
-SHA1 (patch-Makefile) = 3170f9e4405a605f3a349785df13d156c846983d
+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 --git a/htslib/patches/patch-Makefile b/htslib/patches/patch-Makefile
deleted file mode 100644
index 507c441ccd..0000000000
--- a/htslib/patches/patch-Makefile
+++ /dev/null
@@ -1,58 +0,0 @@
-$NetBSD$
-
-# Respect build environment
-
---- Makefile.orig	2020-07-21 09:19:56.000000000 +0000
-+++ Makefile
-@@ -22,25 +22,26 @@
- # 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
-+PREFIX      ?= /usr/local
-+prefix      = $(PREFIX)
- exec_prefix = $(prefix)
- bindir      = $(exec_prefix)/bin
- includedir  = $(prefix)/include
-@@ -69,7 +70,7 @@ BUILT_PROGRAMS = \
- 	htsfile \
- 	tabix
- 
--BUILT_TEST_PROGRAMS = \
-+BUILT_TEST_PROGRAMS ?= \
- 	test/hts_endian \
- 	test/fieldarith \
- 	test/hfile \
-@@ -90,7 +91,7 @@ BUILT_TEST_PROGRAMS = \
- 	test/test-bcf-translate \
- 	test/test-parse-reg
- 
--BUILT_THRASH_PROGRAMS = \
-+BUILT_THRASH_PROGRAMS ?= \
- 	test/thrash_threads1 \
- 	test/thrash_threads2 \
- 	test/thrash_threads3 \