htslib, samtools: Upgrade to latest release

[Jason Bacon <bacon4000%gmail.com@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon4000%gmail.com@localhost>
Pushed By:	outpaddling
Date:		Thu Nov 2 13:29:16 2017 -0500
Changeset:	8bbcf5eed94a1c2c756402e9f41bb73105145314

Modified Files:
	htslib/Makefile
	htslib/PLIST
	htslib/distinfo
	samtools/Makefile
	samtools/distinfo
Removed Files:
	htslib/patches/patch-Makefile
	htslib/patches/patch-hfile__libcurl.c
	htslib/patches/patch-htslib_ksort.h
	samtools/patches/patch-Makefile
	samtools/patches/patch-configure.ac

Log Message:
htslib, samtools: Upgrade to latest release

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=8bbcf5eed94a1c2c756402e9f41bb73105145314

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

diffstat:
 htslib/Makefile                       |  4 +-
 htslib/PLIST                          |  6 ++-
 htslib/distinfo                       | 11 ++---
 htslib/patches/patch-Makefile         | 89 -----------------------------------
 htslib/patches/patch-hfile__libcurl.c | 17 -------
 htslib/patches/patch-htslib_ksort.h   | 38 ---------------
 samtools/Makefile                     |  2 +-
 samtools/distinfo                     | 10 ++--
 samtools/patches/patch-Makefile       | 77 ------------------------------
 samtools/patches/patch-configure.ac   | 22 ---------
 10 files changed, 17 insertions(+), 259 deletions(-)

diffs:
diff --git a/htslib/Makefile b/htslib/Makefile
index 5098f0b778..d0d5af9f72 100644
--- a/htslib/Makefile
+++ b/htslib/Makefile
@@ -28,10 +28,12 @@ SUBST_FILES.version+=	${WRKSRC}/configure.ac
 
 PKGCONFIG_OVERRIDE=	htslib.pc.in
 
-PORTVERSION=	1.3.2
+PORTVERSION=	1.6
 
 pre-configure:
 	cd ${WRKSRC} && autoreconf
 
 .include "../../devel/zlib/buildlink3.mk"
+.include "../../archivers/bzip2/buildlink3.mk"
+.include "../../archivers/xz/buildlink3.mk"
 .include "../../mk/bsd.pkg.mk"
diff --git a/htslib/PLIST b/htslib/PLIST
index a040045fe2..893aff019a 100644
--- a/htslib/PLIST
+++ b/htslib/PLIST
@@ -8,6 +8,9 @@ include/htslib/faidx.h
 include/htslib/hfile.h
 include/htslib/hts.h
 include/htslib/hts_defs.h
+include/htslib/hts_endian.h
+include/htslib/hts_log.h
+include/htslib/hts_os.h
 include/htslib/kbitset.h
 include/htslib/kfunc.h
 include/htslib/khash.h
@@ -21,13 +24,14 @@ include/htslib/regidx.h
 include/htslib/sam.h
 include/htslib/synced_bcf_reader.h
 include/htslib/tbx.h
+include/htslib/thread_pool.h
 include/htslib/vcf.h
 include/htslib/vcf_sweep.h
 include/htslib/vcfutils.h
 lib/libhts.a
 lib/libhts.so
-lib/libhts.so.1
 lib/libhts.so.${PKGVERSION}
+lib/libhts.so.2
 lib/pkgconfig/htslib.pc
 man/man1/htsfile.1
 man/man1/tabix.1
diff --git a/htslib/distinfo b/htslib/distinfo
index 32260aab0c..d7c092663d 100644
--- a/htslib/distinfo
+++ b/htslib/distinfo
@@ -1,9 +1,6 @@
 $NetBSD$
 
-SHA1 (htslib-1.3.2.tar.gz) = 41ce614ac9b9dc751fa25355e8b46a9bd9aa9ace
-RMD160 (htslib-1.3.2.tar.gz) = 6a2a9cfa0fb56bd113891aa4933e6da387a97942
-SHA512 (htslib-1.3.2.tar.gz) = f40f69c895046ab4cbb992f02926d9152b4e8e6a9ba54513f79287477a6b239c47bdb99b8d710c7bbf2f5281266b37c347b0ba5fcb9beff8ba12e53a6acff3f3
-Size (htslib-1.3.2.tar.gz) = 1066181 bytes
-SHA1 (patch-Makefile) = 5508f222237a33afde7474d8b7e6c999641316d6
-SHA1 (patch-hfile__libcurl.c) = 5369ce80563a57917192760e9673398f383bf71e
-SHA1 (patch-htslib_ksort.h) = 67e6d1450026bfe90f4ecb9ca0eae9335f1c3752
+SHA1 (htslib-1.6.tar.gz) = 14281b35dde9d94be16c9986de435de19adba822
+RMD160 (htslib-1.6.tar.gz) = 8a16541cacb7b25a664287b4a1c48d935c3f6d5c
+SHA512 (htslib-1.6.tar.gz) = 5c1a314cae3b106c83f11166e294b94895ed915da010270f239ae52dd77a19039c227bf9f6a7f36894cb9b77f361b2aa6150381487d9a1bc6f1176e7817d34d3
+Size (htslib-1.6.tar.gz) = 1155672 bytes
diff --git a/htslib/patches/patch-Makefile b/htslib/patches/patch-Makefile
deleted file mode 100644
index c37098f6e4..0000000000
--- a/htslib/patches/patch-Makefile
+++ /dev/null
@@ -1,89 +0,0 @@
-$NetBSD$
-
-# Respect build env and filesystem hierarchy
-
---- Makefile.orig	2016-09-13 06:15:37.000000000 +0000
-+++ Makefile
-@@ -22,16 +22,7 @@
- # 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 =
--# TODO: probably update cram code to make it compile cleanly with -Wc++-compat
--CFLAGS   = -g -Wall -O2
- EXTRA_CFLAGS_PIC = -fpic
--LDFLAGS  =
--LIBS     =
- 
- # For now these don't work too well as samtools also needs to know to
- # add -lbz2 and -llzma if linking against the static libhts.a library.
-@@ -58,16 +49,10 @@ includedir  = $(prefix)/include
- libdir      = $(exec_prefix)/lib
- libexecdir  = $(exec_prefix)/libexec
- datarootdir = $(prefix)/share
--mandir      = $(datarootdir)/man
-+mandir      = $(PKGMANDIR)/man
- man1dir     = $(mandir)/man1
- man5dir     = $(mandir)/man5
--pkgconfigdir= $(libdir)/pkgconfig
--
--MKDIR_P = mkdir -p
--INSTALL = install -p
--INSTALL_PROGRAM = $(INSTALL)
--INSTALL_DATA    = $(INSTALL) -m 644
--INSTALL_DIR     = $(MKDIR_P) -m 755
-+pkgconfigdir= $(exec_prefix)/lib/pkgconfig
- 
- # Set by config.mk if plugins are enabled
- plugindir =
-@@ -86,7 +71,7 @@ BUILT_TEST_PROGRAMS = \
- 	test/test-vcf-api \
- 	test/test-vcf-sweep
- 
--all: lib-static lib-shared $(BUILT_PROGRAMS) plugins $(BUILT_TEST_PROGRAMS)
-+all: lib-static lib-shared $(BUILT_PROGRAMS) plugins
- 
- HTSPREFIX =
- include htslib_vars.mk
-@@ -344,23 +329,28 @@ test/test-vcf-sweep.o: test/test-vcf-swe
- 
- 
- install: libhts.a $(BUILT_PROGRAMS) $(BUILT_PLUGINS) installdirs install-$(SHLIB_FLAVOUR) install-pkgconfig
--	$(INSTALL_PROGRAM) $(BUILT_PROGRAMS) $(DESTDIR)$(bindir)
--	if test -n "$(BUILT_PLUGINS)"; then $(INSTALL_PROGRAM) $(BUILT_PLUGINS) $(DESTDIR)$(plugindir); fi
--	$(INSTALL_DATA) htslib/*.h $(DESTDIR)$(includedir)/htslib
--	$(INSTALL_DATA) libhts.a $(DESTDIR)$(libdir)/libhts.a
--	$(INSTALL_DATA) htsfile.1 tabix.1 $(DESTDIR)$(man1dir)
--	$(INSTALL_DATA) faidx.5 sam.5 vcf.5 $(DESTDIR)$(man5dir)
-+	$(BSD_INSTALL_PROGRAM) $(BUILT_PROGRAMS) $(DESTDIR)$(bindir)
-+	if test -n "$(BUILT_PLUGINS)"; then $(BSD_INSTALL_PROGRAM) $(BUILT_PLUGINS) $(DESTDIR)$(plugindir); fi
-+	$(BSD_INSTALL_DATA) htslib/*.h $(DESTDIR)$(includedir)/htslib
-+	$(BSD_INSTALL_DATA) libhts.a $(DESTDIR)$(libdir)/libhts.a
-+	$(BSD_INSTALL_DATA) htsfile.1 tabix.1 $(DESTDIR)$(man1dir)
-+	$(BSD_INSTALL_DATA) faidx.5 sam.5 vcf.5 $(DESTDIR)$(man5dir)
- 
- installdirs:
--	$(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(includedir) $(DESTDIR)$(includedir)/htslib $(DESTDIR)$(libdir) $(DESTDIR)$(man1dir) $(DESTDIR)$(man5dir) $(DESTDIR)$(pkgconfigdir)
--	if test -n "$(plugindir)"; then $(INSTALL_DIR) $(DESTDIR)$(plugindir); fi
-+	$(BSD_INSTALL_PROGRAM_DIR) $(DESTDIR)$(bindir)
-+	$(BSD_INSTALL_LIB_DIR) $(DESTDIR)$(includedir) \
-+		$(DESTDIR)$(includedir)/htslib \
-+		$(DESTDIR)$(libdir) \
-+		$(DESTDIR)$(pkgconfigdir)
-+	$(BSD_INSTALL_MAN_DIR) $(DESTDIR)$(man1dir) $(DESTDIR)$(man5dir)
-+	if test -n "$(plugindir)"; then $(BSD_INSTALL_LIB_DIR) $(DESTDIR)$(plugindir); fi
- 
- # After installation, the real file in $(libdir) will be libhts.so.X.Y.Z,
- # with symlinks libhts.so (used via -lhts during linking of client programs)
- # and libhts.so.NN (used by client executables at runtime).
- 
- install-so: libhts.so installdirs
--	$(INSTALL_DATA) libhts.so $(DESTDIR)$(libdir)/libhts.so.$(PACKAGE_VERSION)
-+	$(BSD_INSTALL_LIB) libhts.so $(DESTDIR)$(libdir)/libhts.so.$(PACKAGE_VERSION)
- 	ln -sf libhts.so.$(PACKAGE_VERSION) $(DESTDIR)$(libdir)/libhts.so
- 	ln -sf libhts.so.$(PACKAGE_VERSION) $(DESTDIR)$(libdir)/libhts.so.$(LIBHTS_SOVERSION)
- 
diff --git a/htslib/patches/patch-hfile__libcurl.c b/htslib/patches/patch-hfile__libcurl.c
deleted file mode 100644
index f7109afc41..0000000000
--- a/htslib/patches/patch-hfile__libcurl.c
+++ /dev/null
@@ -1,17 +0,0 @@
-$NetBSD$
-
-# Portability
-
---- hfile_libcurl.c.orig	2015-12-15 16:34:33 UTC
-+++ hfile_libcurl.c
-@@ -39,6 +39,10 @@ DEALINGS IN THE SOFTWARE.  */
- 
- #include <curl/curl.h>
- 
-+#ifndef ENOTRECOVERABLE
-+#define ENOTRECOVERABLE EIO
-+#endif
-+
- typedef struct {
-     hFILE base;
-     CURL *easy;
diff --git a/htslib/patches/patch-htslib_ksort.h b/htslib/patches/patch-htslib_ksort.h
deleted file mode 100644
index 61f3bf2a44..0000000000
--- a/htslib/patches/patch-htslib_ksort.h
+++ /dev/null
@@ -1,38 +0,0 @@
-$NetBSD$
-
-# NetBSD expands uintXX_t to __unitXX_t, causing undefined refs.
-# See comments in patch below.
---- htslib/ksort.h.orig	2017-05-19 15:11:35.000000000 +0000
-+++ htslib/ksort.h
-@@ -63,6 +63,7 @@
- 
- #include <stdlib.h>
- #include <string.h>
-+#include <stdint.h>
- 
- typedef struct {
- 	void *left, *right;
-@@ -266,13 +267,21 @@ typedef struct {
- 	}
- 
- #define ks_mergesort(name, n, a, t) ks_mergesort_##name(n, a, t)
--#define ks_introsort(name, n, a) ks_introsort_##name(n, a)
-+/* NetBSD has typedef __uint32_t uint32_t.  Pass name through another
-+   level of expansion as done by KSORT_INIT_GENERIC so the cpp output
-+   will match. Otherwise, we get undefined referencas. */
-+#define __ks_introsort(name, n, a) ks_introsort_##name(n, a)
-+#define ks_introsort(name, n, a) __ks_introsort(name,n, a)
- #define ks_combsort(name, n, a) ks_combsort_##name(n, a)
- #define ks_heapsort(name, n, a) ks_heapsort_##name(n, a)
- #define ks_heapmake(name, n, a) ks_heapmake_##name(n, a)
- #define ks_heapadjust(name, i, n, a) ks_heapadjust_##name(i, n, a)
- #define ks_ksmall(name, n, a, k) ks_ksmall_##name(n, a, k)
--#define ks_shuffle(name, n, a) ks_shuffle_##name(n, a)
-+/* NetBSD has typedef __uint32_t uint32_t.  Pass name through another
-+   level of expansion as done by KSORT_INIT_GENERIC so the cpp output
-+   will match. Otherwise, we get undefined referencas. */
-+#define __ks_shuffle(name, n, a) ks_shuffle_##name(n, a)
-+#define ks_shuffle(name, n, a) __ks_shuffle(name,n, a)
- 
- #define ks_lt_generic(a, b) ((a) < (b))
- #define ks_lt_str(a, b) (strcmp((a), (b)) < 0)
diff --git a/samtools/Makefile b/samtools/Makefile
index 8a643c7b2c..587d29e4de 100644
--- a/samtools/Makefile
+++ b/samtools/Makefile
@@ -22,7 +22,7 @@ GNU_CONFIGURE=	yes
 REPLACE_PERL=	misc/*.pl misc/plot-bamstats test/test.pl
 REPLACE_PYTHON=	misc/*.py
 
-PORTVERSION=	1.3.1
+PORTVERSION=	1.6
 
 post-patch:
 	${CP} ${FILESDIR}/ax_with_htslib.m4 ${WRKSRC}/
diff --git a/samtools/distinfo b/samtools/distinfo
index 1639e69314..3190366247 100644
--- a/samtools/distinfo
+++ b/samtools/distinfo
@@ -1,8 +1,6 @@
 $NetBSD$
 
-SHA1 (samtools-1.3.1.tar.gz) = 1d5d2bca1742115ed0bc950b9c21132e9872768d
-RMD160 (samtools-1.3.1.tar.gz) = 8c559e3e4e548e8b8858e10b05ecf59e6d370101
-SHA512 (samtools-1.3.1.tar.gz) = 9ad5a7e25db73454c7f7661ebbfba372cfaa86f543d57302736a0021adefe068e6571d8095e13d0faa37a63c2051636b7ac232463117540b0d7571391af7cfb1
-Size (samtools-1.3.1.tar.gz) = 3757176 bytes
-SHA1 (patch-Makefile) = bf0bd9cbce2f5c5c91f0c704fd7dc1aa1f12e61a
-SHA1 (patch-configure.ac) = 8a37d938d49f7def394dd3f73a41e139151cad4a
+SHA1 (samtools-1.6.tar.gz) = d44b49e0b9bd6324c2cd21de31edb2f199720a28
+RMD160 (samtools-1.6.tar.gz) = ff4814f1399e63196ff62bce0aef085d2105bda7
+SHA512 (samtools-1.6.tar.gz) = c7729f7f0caecc1347f76f4e3375b5b6e6506488c65dbc068a7f62509bd17b1ee177cef6c828fb9d4a430f711051170f60f593aaca3969b1be3c6cefbae21726
+Size (samtools-1.6.tar.gz) = 4014195 bytes
diff --git a/samtools/patches/patch-Makefile b/samtools/patches/patch-Makefile
deleted file mode 100644
index 287273644a..0000000000
--- a/samtools/patches/patch-Makefile
+++ /dev/null
@@ -1,77 +0,0 @@
-$NetBSD$
-
-# Respect build env
---- Makefile.orig	2016-04-22 09:22:44.000000000 +0000
-+++ Makefile
-@@ -21,10 +21,10 @@
- # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
- # DEALINGS IN THE SOFTWARE.
- 
--CC       = gcc
--CPPFLAGS =
--CFLAGS   = -g -Wall -O2
--LDFLAGS  =
-+CC       ?= gcc
-+CPPFLAGS ?=
-+CFLAGS   ?= -g -Wall -O2
-+LDFLAGS  ?=
- LIBS     =
- 
- LOBJS=      bam_aux.o bam.o bam_import.o sam.o \
-@@ -38,20 +38,13 @@ AOBJS=      bam_index.o bam_plcmd.o sam_
-             bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o \
-             bam_quickcheck.o bam_addrprg.o
- 
--prefix      = /usr/local
-+prefix      = $(STAGEDIR)$(PREFIX)
- exec_prefix = $(prefix)
- bindir      = $(exec_prefix)/bin
- datarootdir = $(prefix)/share
--mandir      = $(datarootdir)/man
-+mandir      = $(PKGMANDIR)/man
- man1dir     = $(mandir)/man1
- 
--MKDIR_P = mkdir -p
--INSTALL = install -p
--INSTALL_PROGRAM = $(INSTALL)
--INSTALL_DATA    = $(INSTALL) -m 644
--INSTALL_DIR     = $(MKDIR_P) -m 755
--
--
- PROGRAMS = samtools
- 
- BUILT_MISC_PROGRAMS = \
-@@ -59,7 +52,6 @@ BUILT_MISC_PROGRAMS = \
- 	misc/md5fa misc/md5sum-lite misc/wgsim
- 
- MISC_PROGRAMS = \
--	$(BUILT_MISC_PROGRAMS) \
- 	misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl \
- 	misc/interpolate_sam.pl misc/novo2sam.pl \
- 	misc/plot-bamstats misc/psl2sam.pl \
-@@ -82,7 +74,7 @@ all: $(PROGRAMS) $(BUILT_MISC_PROGRAMS) 
- # TODO Use configure or htslib.pc to add -rdynamic/-ldl conditionally
- ALL_CPPFLAGS = -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS)
- ALL_LDFLAGS  = -rdynamic $(HTSLIB_LDFLAGS) $(LDFLAGS)
--ALL_LIBS     = -lz -ldl $(LIBS)
-+ALL_LIBS     = -lz $(LIBS)
- 
- # Usually config.mk and config.h are generated by running configure
- # or config.status, but if those aren't used create defaults here.
-@@ -280,10 +272,12 @@ misc/maq2sam-long.o: misc/maq2sam.c conf
- 
- 
- install: $(PROGRAMS) $(BUILT_MISC_PROGRAMS)
--	$(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(man1dir)
--	$(INSTALL_PROGRAM) $(PROGRAMS) $(MISC_PROGRAMS) $(DESTDIR)$(bindir)
--	$(INSTALL_DATA) samtools.1 misc/wgsim.1 $(DESTDIR)$(man1dir)
--
-+	$(BSD_INSTALL_PROGRAM_DIR) $(DESTDIR)$(bindir)
-+	$(BSD_INSTALL_MAN_DIR) $(DESTDIR)$(man1dir) 
-+	$(BSD_INSTALL_PROGRAM) $(PROGRAMS) $(DESTDIR)$(bindir)
-+	$(BSD_INSTALL_PROGRAM) $(BUILT_MISC_PROGRAMS) $(DESTDIR)$(bindir)
-+	$(BSD_INSTALL_SCRIPT) $(MISC_PROGRAMS) $(DESTDIR)$(bindir)
-+	$(BSD_INSTALL_DATA) samtools.1 misc/wgsim.1 $(DESTDIR)$(man1dir)
- 
- testclean:
- 	-rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.*
diff --git a/samtools/patches/patch-configure.ac b/samtools/patches/patch-configure.ac
deleted file mode 100644
index 33645329cf..0000000000
--- a/samtools/patches/patch-configure.ac
+++ /dev/null
@@ -1,22 +0,0 @@
-$NetBSD$
-
-# Replace non-portable version check and add deps to configure script
---- configure.ac.orig	2015-12-15 21:26:20 UTC
-+++ configure.ac
-@@ -23,12 +23,15 @@
- # DEALINGS IN THE SOFTWARE.
- 
- dnl Process this file with autoconf to produce a configure script
--AC_INIT([Samtools], m4_esyscmd_s([make print-version]),
-+AC_INIT([Samtools], [1.3.1],
-         [samtools-help%lists.sourceforge.net@localhost], [], [http://www.htslib.org/])
- AC_PREREQ([2.63])  dnl This version introduced 4-argument AC_CHECK_HEADER
- AC_CONFIG_SRCDIR([bamtk.c])
- AC_CONFIG_HEADERS([config.h])
- 
-+m4_include([ax_with_htslib.m4])
-+m4_include([ax_with_curses.m4])
-+
- dnl Copyright notice to be copied into the generated configure script
- AC_COPYRIGHT([Portions copyright (C) 2015 Genome Research Ltd.
-