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Date:      Wed, 25 Oct 2017 10:19:50 +0000 (UTC)
From:      Luca Pizzamiglio <pizzamig@FreeBSD.org>
To:        ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org
Subject:   svn commit: r452840 - in head/biology: bcftools bcftools/files htslib htslib/files samtools samtools/files
Message-ID:  <201710251019.v9PAJolt086771@repo.freebsd.org>

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Author: pizzamig
Date: Wed Oct 25 10:19:50 2017
New Revision: 452840
URL: https://svnweb.freebsd.org/changeset/ports/452840

Log:
  biology/htslib biology/bcftools biology/samtools: Update to 1.6
  
  PR:		223094
  Submitted by:	mzaki@niid.go.jp
  Approved by:	cartwright@asu.edu (maintainer)
  Approved by:	olivier (mentor)
  Differential Revision:	https://reviews.freebsd.org/D12768

Added:
  head/biology/bcftools/files/patch-configure.ac   (contents, props changed)
  head/biology/bcftools/files/patch-misc_run-roh.pl   (contents, props changed)
Deleted:
  head/biology/htslib/files/patch-configure.ac
  head/biology/samtools/files/ax_with_curses.m4
  head/biology/samtools/files/ax_with_htslib.m4
  head/biology/samtools/files/patch-configure.ac
  head/biology/samtools/files/patch-dict.c
  head/biology/samtools/files/patch-errmod.c
Modified:
  head/biology/bcftools/Makefile
  head/biology/bcftools/distinfo
  head/biology/bcftools/files/patch-Makefile
  head/biology/bcftools/files/patch-prob1.c
  head/biology/bcftools/files/patch-test_test.pl
  head/biology/bcftools/files/pkg-message.in
  head/biology/bcftools/pkg-plist
  head/biology/htslib/Makefile
  head/biology/htslib/distinfo
  head/biology/htslib/files/patch-Makefile
  head/biology/htslib/files/patch-hfile__libcurl.c
  head/biology/htslib/pkg-plist
  head/biology/samtools/Makefile
  head/biology/samtools/distinfo
  head/biology/samtools/files/patch-Makefile
  head/biology/samtools/files/patch-test_test.pl
  head/biology/samtools/files/pkg-message.in

Modified: head/biology/bcftools/Makefile
==============================================================================
--- head/biology/bcftools/Makefile	Wed Oct 25 10:12:26 2017	(r452839)
+++ head/biology/bcftools/Makefile	Wed Oct 25 10:19:50 2017	(r452840)
@@ -2,8 +2,7 @@
 # $FreeBSD$
 
 PORTNAME=	bcftools
-PORTVERSION=	1.3.1
-PORTREVISION=	2
+PORTVERSION=	1.6
 CATEGORIES=	biology
 
 MAINTAINER=	cartwright@asu.edu
@@ -12,7 +11,7 @@ COMMENT=	Tools for manipulating next-generation sequen
 LICENSE=	MIT
 # LICENSE_FILE=	${WRKSRC}/LICENSE
 
-BUILD_DEPENDS=	htslib>=1.3:biology/htslib
+BUILD_DEPENDS=	htslib>=1.6:biology/htslib
 LIB_DEPENDS=	libhts.so:biology/htslib
 TEST_DEPENDS=	bash:shells/bash
 
@@ -21,10 +20,12 @@ CONFLICTS_BUILD=openssl
 USE_GITHUB=	yes
 GH_ACCOUNT=	samtools
 
-USES=		gmake perl5 shebangfix
+USES=		autoreconf gmake perl5 python shebangfix
 USE_PERL5=	test
+PYTHON_NO_DEPENDS=	yes
+GNU_CONFIGURE=	yes
 SUB_FILES=	pkg-message
-SHEBANG_FILES=	vcfutils.pl plot-vcfstats plugins/color-chrs.pl test/test.pl
+SHEBANG_FILES=	misc/* test/test.pl
 
 OPTIONS_DEFINE=	GPL
 GPL_DESC=	Enable modules that rely on GPL code
@@ -37,19 +38,15 @@ GPL_LIB_DEPENDS=	libgsl.so:math/gsl
 CPPFLAGS+=	-I${LOCALBASE}/include
 LDFLAGS+=	-L${LOCALBASE}/lib
 
-MAKE_ENV=	INSTALL_LIB="${INSTALL_LIB}" \
-		INSTALL_DATA="${INSTALL_DATA}" \
-		INSTALL_PROGRAM="${INSTALL_PROGRAM}" \
-		INSTALL_SCRIPT="${INSTALL_SCRIPT}" \
-		INSTALL_DIR="${MKDIR}"
-
 .if ${PORT_OPTIONS:MGPL}
 MAKE_ENV+=	USE_GPL=1
 LICENSE=	GPLv3
 .endif
 
-PLIST_SUB=	PORTVERSION="${PORTVERSION}"
-
 TEST_TARGET=	test
+
+post-patch:
+	@${GREP} -q '@PORTVERSION@' ${WRKSRC}/configure.ac || (echo "@PORTVERSION@ in file/patch-configure.ac is overwritten probably due to using 'make makepatch'"; exit 1)
+	@${REINPLACE_CMD} -e 's|@PORTVERSION@|${PORTVERSION}|g' ${WRKSRC}/configure.ac
 
 .include <bsd.port.mk>

Modified: head/biology/bcftools/distinfo
==============================================================================
--- head/biology/bcftools/distinfo	Wed Oct 25 10:12:26 2017	(r452839)
+++ head/biology/bcftools/distinfo	Wed Oct 25 10:19:50 2017	(r452840)
@@ -1,3 +1,3 @@
-TIMESTAMP = 1463692643
-SHA256 (samtools-bcftools-1.3.1_GH0.tar.gz) = 99a5cc05faa974f5ddbeebf346bb51a806bdaaf8e2f6adc3bead28551983e77e
-SIZE (samtools-bcftools-1.3.1_GH0.tar.gz) = 958207
+TIMESTAMP = 1508307708
+SHA256 (samtools-bcftools-1.6_GH0.tar.gz) = afb2a96d3419fbe77fab5c501dc28bc5e691145353ac5600909a75c0e625f025
+SIZE (samtools-bcftools-1.6_GH0.tar.gz) = 2333330

Modified: head/biology/bcftools/files/patch-Makefile
==============================================================================
--- head/biology/bcftools/files/patch-Makefile	Wed Oct 25 10:12:26 2017	(r452839)
+++ head/biology/bcftools/files/patch-Makefile	Wed Oct 25 10:19:50 2017	(r452840)
@@ -1,19 +1,9 @@
---- Makefile.orig	2015-12-15 21:42:34 UTC
+--- Makefile.orig	2017-09-28 11:22:48 UTC
 +++ Makefile
-@@ -29,16 +29,15 @@ TEST_PROG=  test/test-rbuf
- all: $(PROG) $(TEST_PROG)
+@@ -22,10 +22,10 @@
+ # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+ # DEALINGS IN THE SOFTWARE.
  
- # Adjust $(HTSDIR) to point to your top-level htslib directory
--HTSDIR = ../htslib
--include $(HTSDIR)/htslib.mk
--HTSLIB = $(HTSDIR)/libhts.a
--BGZIP  = $(HTSDIR)/bgzip
--TABIX  = $(HTSDIR)/tabix
-+HTSDIR = $(prefix)/include
-+HTSLIB = -lhts
-+BGZIP  = $(HTSDIR)/../bin/bgzip
-+TABIX  = $(HTSDIR)/../bin/tabix
- 
 -CC       = gcc
 -CPPFLAGS =
 -CFLAGS   = -g -Wall -Wc++-compat -O2
@@ -24,17 +14,13 @@
 +LDFLAGS  +=
  LIBS     =
  
- OBJS     = main.o vcfindex.o tabix.o \
-@@ -57,26 +56,20 @@ GSL_LIBS       =
- ifdef USE_GPL
-     EXTRA_CPPFLAGS += -DUSE_GPL
-     OBJS += polysomy.o peakfit.o
--    GSL_LIBS = -lgsl -lcblas
-+    GSL_LIBS = -lgsl -lgslcblas
- endif
+ DYNAMIC_FLAGS = -rdynamic
+@@ -42,26 +42,25 @@ OBJS     = main.o vcfindex.o tabix.o \
+            vcfsort.o \
+            ccall.o em.o prob1.o kmin.o # the original samtools calling
  
 -prefix      = /usr/local
-+prefix      = ${STAGEDIR}${PREFIX}
++prefix      = ${PREFIX}
  exec_prefix = $(prefix)
  bindir      = $(exec_prefix)/bin
  libdir      = $(exec_prefix)/lib
@@ -42,37 +28,52 @@
 -mandir      = $(prefix)/share/man
 +mandir      = $(prefix)/man
  man1dir     = $(mandir)/man1
- 
+ # Installation location for $(PLUGINS)
  plugindir   = $(libexecdir)/bcftools
  pluginpath  = $(plugindir)
+ # Installation location for $(MISC_PROGRAMS) and $(MISC_SCRIPTS)
+-misc_bindir = $(bindir)
++misc_bindir = $(bindir)/samtools_misc
  
--MKDIR_P = mkdir -p
+ MKDIR_P = mkdir -p
 -INSTALL = install -p
--INSTALL_PROGRAM = $(INSTALL)
 -INSTALL_DATA    = $(INSTALL) -m 644
 -INSTALL_DIR     = $(MKDIR_P) -m 755
--
- MISC_PROGRAMS = plot-vcfstats vcfutils.pl plugins/color-chrs.pl
+-INSTALL_MAN     = $(INSTALL_DATA)
+-INSTALL_PROGRAM = $(INSTALL)
+-INSTALL_SCRIPT  = $(INSTALL_PROGRAM)
++INSTALL_DATA    = ${BSD_INSTALL_DATA}
++INSTALL_DIR     = $(MKDIR_P)
++INSTALL_MAN     = ${BSD_INSTALL_MAN}
++INSTALL_PROGRAM = ${BSD_INSTALL_PROGRAM}
++INSTALL_SCRIPT  = ${BSD_INSTALL_SCRIPT}
  
- all:$(PROG) plugins
-@@ -181,7 +174,7 @@ test/test-rbuf: test/test-rbuf.o
- 	$(CC) $(LDFLAGS) -o $@ $^ -lm $(LIBS)
+ PROGRAMS = bcftools
+ MISC_SCRIPTS = \
+@@ -77,7 +76,7 @@ all: $(PROGRAMS) $(TEST_PROGRAMS) plugin
  
- bcftools: $(HTSLIB) $(OBJS)
--	$(CC) -rdynamic $(LDFLAGS) -o $@ $(OBJS) $(HTSLIB) -lpthread -lz -lm -ldl $(GSL_LIBS) $(LIBS)
-+	$(CC) -rdynamic $(LDFLAGS) -o $@ $(OBJS) $(HTSLIB) -pthread -lz -lm $(GSL_LIBS) $(LIBS)
+ ALL_CPPFLAGS = -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS)
+ ALL_LDFLAGS  = $(HTSLIB_LDFLAGS) $(LDFLAGS)
+-ALL_LIBS     = -lz -ldl $(LIBS)
++ALL_LIBS     = -lz $(LIBS)
  
- doc/bcftools.1: doc/bcftools.txt
- 	cd doc && a2x -adate="$(DOC_DATE)" -aversion=$(DOC_VERSION) --doctype manpage --format manpage bcftools.txt
-@@ -198,8 +191,9 @@ docs: doc/bcftools.1 doc/bcftools.html
+ # Usually config.mk and config.h are generated by running configure
+ # or config.status, but if those aren't used create defaults here.
+@@ -131,7 +130,7 @@ print-version:
+ ifdef USE_GPL
+     main.o : EXTRA_CPPFLAGS += -DUSE_GPL
+     OBJS += polysomy.o peakfit.o
+-    GSL_LIBS ?= -lgsl -lcblas
++    GSL_LIBS ?= -lgsl -lgslcblas
+ endif
+ 
+ bcftools: $(OBJS) $(HTSLIB)
+@@ -273,7 +272,7 @@ docs: doc/bcftools.1 doc/bcftools.html
  # Since there is no make dependency, bcftools.1 can be out-of-date and
  # make docs can be run to update if asciidoc is available
- install: $(PROG)
+ install: $(PROG) $(PLUGINS)
 -	$(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(man1dir) $(DESTDIR)$(plugindir)
--	$(INSTALL_PROGRAM) $(PROG) $(MISC_PROGRAMS) $(DESTDIR)$(bindir)
-+	$(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(bindir)/samtools_misc $(DESTDIR)$(man1dir) $(DESTDIR)$(plugindir)
-+	$(INSTALL_PROGRAM) $(PROG) $(DESTDIR)$(bindir)
-+	$(INSTALL_SCRIPT) $(MISC_PROGRAMS) $(DESTDIR)$(bindir)/samtools_misc
- 	$(INSTALL_DATA) doc/bcftools.1 $(DESTDIR)$(man1dir)
- 	$(INSTALL_PROGRAM) plugins/*.so $(DESTDIR)$(plugindir)
- 
++	$(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(misc_bindir) $(DESTDIR)$(man1dir) $(DESTDIR)$(plugindir)
+ 	$(INSTALL_PROGRAM) $(PROGRAMS) $(DESTDIR)$(bindir)
+ 	$(INSTALL_SCRIPT) $(MISC_SCRIPTS) $(DESTDIR)$(misc_bindir)
+ 	$(INSTALL_MAN) doc/bcftools.1 $(DESTDIR)$(man1dir)

Added: head/biology/bcftools/files/patch-configure.ac
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/bcftools/files/patch-configure.ac	Wed Oct 25 10:19:50 2017	(r452840)
@@ -0,0 +1,11 @@
+--- configure.ac.orig	2017-09-28 11:22:48 UTC
++++ configure.ac
+@@ -23,7 +23,7 @@
+ # DEALINGS IN THE SOFTWARE.
+ 
+ dnl Process this file with autoconf to produce a configure script
+-AC_INIT([BCFtools], m4_esyscmd_s([make print-version]),
++AC_INIT([BCFtools], [@PORTVERSION@],
+         [samtools-help@lists.sourceforge.net], [], [http://www.htslib.org/])
+ AC_PREREQ([2.63])  dnl This version introduced 4-argument AC_CHECK_HEADER
+ AC_CONFIG_SRCDIR([main.c])

Added: head/biology/bcftools/files/patch-misc_run-roh.pl
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/bcftools/files/patch-misc_run-roh.pl	Wed Oct 25 10:19:50 2017	(r452840)
@@ -0,0 +1,11 @@
+--- misc/run-roh.pl.orig	2017-10-18 09:33:24 UTC
++++ misc/run-roh.pl
+@@ -97,7 +97,7 @@ sub cmd
+     else 
+     {      
+         # child
+-        exec('/bin/bash', '-o','pipefail','-c', $cmd) or error("Failed to run the command [/bin/sh -o pipefail -c $cmd]: $!");
++        exec('/bin/sh', '-c', $cmd) or error("Failed to run the command [/bin/sh -c $cmd]: $!");
+     }
+ 
+     if ( exists($args{exit_on_error}) && !$args{exit_on_error} ) { return @out; }

Modified: head/biology/bcftools/files/patch-prob1.c
==============================================================================
--- head/biology/bcftools/files/patch-prob1.c	Wed Oct 25 10:12:26 2017	(r452839)
+++ head/biology/bcftools/files/patch-prob1.c	Wed Oct 25 10:19:50 2017	(r452840)
@@ -1,4 +1,4 @@
---- prob1.c.orig	2015-12-15 21:42:34 UTC
+--- prob1.c.orig	2017-09-28 11:22:48 UTC
 +++ prob1.c
 @@ -33,6 +33,12 @@ THE SOFTWARE.  */
  #include <zlib.h>

Modified: head/biology/bcftools/files/patch-test_test.pl
==============================================================================
--- head/biology/bcftools/files/patch-test_test.pl	Wed Oct 25 10:12:26 2017	(r452839)
+++ head/biology/bcftools/files/patch-test_test.pl	Wed Oct 25 10:19:50 2017	(r452840)
@@ -1,6 +1,6 @@
---- test/test.pl.orig	2015-12-22 22:45:13 UTC
+--- test/test.pl.orig	2017-10-18 09:33:24 UTC
 +++ test/test.pl
-@@ -290,7 +290,7 @@ sub _cmd
+@@ -381,7 +381,7 @@ sub _cmd
      else
      {
          # child
@@ -9,7 +9,7 @@
      }
      return ($? >> 8, join('',@out));
  }
-@@ -657,7 +657,7 @@ sub test_usage
+@@ -782,7 +782,7 @@ sub test_usage
      my $command = $args{cmd};
      my $commandpath = $$opts{bin}."/".$command;
      my ($ret,$out) = _cmd("$commandpath $args{redirection} 2>&1");
@@ -18,7 +18,7 @@
  
      my @sections = ($out =~ m/(^[A-Za-z]+.*?)(?:(?=^[A-Za-z]+:)|\z)/msg);
  
-@@ -708,7 +708,7 @@ sub test_usage_subcommand
+@@ -833,7 +833,7 @@ sub test_usage_subcommand
      my $subcommand = $args{subcmd};
      my $commandpath = $$opts{bin}."/".$command;
      my ($ret,$out) = _cmd("$commandpath $subcommand $args{redirection} 2>&1");

Modified: head/biology/bcftools/files/pkg-message.in
==============================================================================
--- head/biology/bcftools/files/pkg-message.in	Wed Oct 25 10:12:26 2017	(r452839)
+++ head/biology/bcftools/files/pkg-message.in	Wed Oct 25 10:19:50 2017	(r452840)
@@ -3,5 +3,5 @@ The miscellaneous tools included with Bcftools have be
 
 Add that directory to your path if you want to use these tools.
 
-Some of these tools depend on Perl5, and it will need to be installed to
+Some of these tools depend on Perl5/Python, and it will need to be installed to
 use them.

Modified: head/biology/bcftools/pkg-plist
==============================================================================
--- head/biology/bcftools/pkg-plist	Wed Oct 25 10:12:26 2017	(r452839)
+++ head/biology/bcftools/pkg-plist	Wed Oct 25 10:19:50 2017	(r452840)
@@ -1,19 +1,32 @@
 bin/bcftools
 bin/samtools_misc/color-chrs.pl
+bin/samtools_misc/guess-ploidy.py
+bin/samtools_misc/plot-roh.py
 bin/samtools_misc/plot-vcfstats
+bin/samtools_misc/run-roh.pl
 bin/samtools_misc/vcfutils.pl
 libexec/bcftools/GTisec.so
+libexec/bcftools/GTsubset.so
+libexec/bcftools/ad-bias.so
+libexec/bcftools/af-dist.so
+libexec/bcftools/check-ploidy.so
+libexec/bcftools/check-sparsity.so
 libexec/bcftools/color-chrs.so
 libexec/bcftools/counts.so
 libexec/bcftools/dosage.so
 libexec/bcftools/fill-AN-AC.so
+libexec/bcftools/fill-from-fasta.so
 libexec/bcftools/fill-tags.so
 libexec/bcftools/fixploidy.so
+libexec/bcftools/fixref.so
 libexec/bcftools/frameshifts.so
+libexec/bcftools/guess-ploidy.so
 libexec/bcftools/impute-info.so
+libexec/bcftools/isecGT.so
 libexec/bcftools/mendelian.so
 libexec/bcftools/missing2ref.so
+libexec/bcftools/prune.so
 libexec/bcftools/setGT.so
 libexec/bcftools/tag2tag.so
-libexec/bcftools/vcf2sex.so
+libexec/bcftools/trio-switch-rate.so
 man/man1/bcftools.1.gz

Modified: head/biology/htslib/Makefile
==============================================================================
--- head/biology/htslib/Makefile	Wed Oct 25 10:12:26 2017	(r452839)
+++ head/biology/htslib/Makefile	Wed Oct 25 10:19:50 2017	(r452840)
@@ -2,7 +2,7 @@
 # $FreeBSD$
 
 PORTNAME=	htslib
-PORTVERSION=	1.3.1
+PORTVERSION=	1.6
 CATEGORIES=	biology devel
 
 MAINTAINER=	cartwright@asu.edu
@@ -34,16 +34,8 @@ CURL_CONFIGURE_ENABLE=	libcurl
 CPPFLAGS+=	-I${LOCALBASE}/include
 LDFLAGS+=	-L${LOCALBASE}/lib
 
-MAKE_ENV=	INSTALL_LIB="${INSTALL_LIB}" \
-		INSTALL_DATA="${INSTALL_DATA}" \
-		INSTALL_PROGRAM="${INSTALL_PROGRAM}" \
-		INSTALL_DIR="${MKDIR}"
-
 PLIST_SUB=	PORTVERSION="${PORTVERSION}"
 
 TEST_TARGET=	test
-
-post-patch:
-	@${REINPLACE_CMD} -e 's|@PORTVERSION@|${PORTVERSION}|g' ${WRKSRC}/configure.ac
 
 .include <bsd.port.mk>

Modified: head/biology/htslib/distinfo
==============================================================================
--- head/biology/htslib/distinfo	Wed Oct 25 10:12:26 2017	(r452839)
+++ head/biology/htslib/distinfo	Wed Oct 25 10:19:50 2017	(r452840)
@@ -1,3 +1,3 @@
-TIMESTAMP = 1463688817
-SHA256 (samtools-htslib-1.3.1_GH0.tar.gz) = 3bbd04f9a0c4c301abd5d19a81920894ac2ee5e86e8aa977e8c2035e01d93ea7
-SIZE (samtools-htslib-1.3.1_GH0.tar.gz) = 1065840
+TIMESTAMP = 1508301522
+SHA256 (samtools-htslib-1.6_GH0.tar.gz) = 4215c9153c27603cbaaf542f2ec128c5e839380d6df6edd4dbf67955170740c6
+SIZE (samtools-htslib-1.6_GH0.tar.gz) = 1155672

Modified: head/biology/htslib/files/patch-Makefile
==============================================================================
--- head/biology/htslib/files/patch-Makefile	Wed Oct 25 10:12:26 2017	(r452839)
+++ head/biology/htslib/files/patch-Makefile	Wed Oct 25 10:19:50 2017	(r452840)
@@ -1,6 +1,6 @@
---- Makefile.orig	2016-04-22 08:45:12 UTC
+--- Makefile.orig	2017-10-18 08:03:33 UTC
 +++ Makefile
-@@ -22,16 +22,7 @@
+@@ -22,41 +22,26 @@
  # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
  # DEALINGS IN THE SOFTWARE.
  
@@ -8,16 +8,23 @@
 -AR     = ar
 -RANLIB = ranlib
 -
+-# Default libraries to link if configure is not used
+-htslib_default_libs = -lz -lm -lbz2 -llzma
+-
 -CPPFLAGS =
 -# 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 -D__FUNCTION__=__func__
 -CFLAGS   = -g -Wall -O2
  EXTRA_CFLAGS_PIC = -fpic
 -LDFLAGS  =
--LIBS     =
+-LIBS     = $(htslib_default_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.
-@@ -58,17 +49,11 @@ includedir  = $(prefix)/include
+-prefix      = /usr/local
++prefix      = ${PREFIX}
+ exec_prefix = $(prefix)
+ bindir      = $(exec_prefix)/bin
+ includedir  = $(prefix)/include
  libdir      = $(exec_prefix)/lib
  libexecdir  = $(exec_prefix)/libexec
  datarootdir = $(prefix)/share
@@ -27,30 +34,27 @@
  man5dir     = $(mandir)/man5
  pkgconfigdir= $(prefix)/libdata/pkgconfig
  
--MKDIR_P = mkdir -p
+ MKDIR_P = mkdir -p
 -INSTALL = install -p
--INSTALL_PROGRAM = $(INSTALL)
 -INSTALL_DATA    = $(INSTALL) -m 644
 -INSTALL_DIR     = $(MKDIR_P) -m 755
--
+-INSTALL_LIB     = $(INSTALL_DATA)
+-INSTALL_MAN     = $(INSTALL_DATA)
+-INSTALL_PROGRAM = $(INSTALL)
++INSTALL_DATA    = ${BSD_INSTALL_DATA}
++INSTALL_DIR     = $(MKDIR_P)
++INSTALL_LIB     = ${BSD_INSTALL_LIB}
++INSTALL_MAN     = ${BSD_INSTALL_MAN}
++INSTALL_PROGRAM = ${BSD_INSTALL_PROGRAM}
+ 
  # Set by config.mk if plugins are enabled
  plugindir =
+@@ -87,7 +72,7 @@ BUILT_THRASH_PROGRAMS = \
+ 	test/thrash_threads5 \
+ 	test/thrash_threads6
  
-@@ -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
-@@ -360,7 +345,7 @@ installdirs:
- # 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)
-+	$(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)
- 

Modified: head/biology/htslib/files/patch-hfile__libcurl.c
==============================================================================
--- head/biology/htslib/files/patch-hfile__libcurl.c	Wed Oct 25 10:12:26 2017	(r452839)
+++ head/biology/htslib/files/patch-hfile__libcurl.c	Wed Oct 25 10:19:50 2017	(r452840)
@@ -1,13 +1,13 @@
---- hfile_libcurl.c.orig	2015-12-15 16:34:33 UTC
+--- hfile_libcurl.c.orig	2017-09-28 11:20:23 UTC
 +++ hfile_libcurl.c
-@@ -39,6 +39,10 @@ DEALINGS IN THE SOFTWARE.  */
+@@ -49,6 +49,10 @@ typedef struct {
+     unsigned int size;
+ } hdrlist;
  
- #include <curl/curl.h>
- 
 +#ifndef ENOTRECOVERABLE
 +#define ENOTRECOVERABLE EIO
 +#endif
 +
  typedef struct {
-     hFILE base;
-     CURL *easy;
+     hdrlist fixed;                   // List of headers supplied at hopen()
+     hdrlist extra;                   // List of headers from callback

Modified: head/biology/htslib/pkg-plist
==============================================================================
--- head/biology/htslib/pkg-plist	Wed Oct 25 10:12:26 2017	(r452839)
+++ head/biology/htslib/pkg-plist	Wed Oct 25 10:19:50 2017	(r452840)
@@ -7,6 +7,9 @@ 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
@@ -20,13 +23,14 @@ 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.%%PORTVERSION%%
+lib/libhts.so.2
 libdata/pkgconfig/htslib.pc
 man/man1/htsfile.1.gz
 man/man1/tabix.1.gz

Modified: head/biology/samtools/Makefile
==============================================================================
--- head/biology/samtools/Makefile	Wed Oct 25 10:12:26 2017	(r452839)
+++ head/biology/samtools/Makefile	Wed Oct 25 10:19:50 2017	(r452840)
@@ -2,7 +2,7 @@
 # $FreeBSD$
 
 PORTNAME=	samtools
-PORTVERSION=	1.3.1
+PORTVERSION=	1.6
 CATEGORIES=	biology
 
 MAINTAINER=	cartwright@asu.edu
@@ -11,34 +11,22 @@ COMMENT=	Tools for manipulating next-generation sequen
 LICENSE=	MIT
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
-BUILD_DEPENDS=	htslib>=1.3:biology/htslib
+BUILD_DEPENDS=	htslib>=1.6:biology/htslib
 LIB_DEPENDS=	libhts.so:biology/htslib
 TEST_DEPENDS=	bash:shells/bash
 
 USE_GITHUB=	yes
 
-USES=		autoreconf gmake ncurses perl5 shebangfix
+USES=		autoreconf gmake ncurses perl5 python shebangfix
 USE_PERL5=	test
+PYTHON_NO_DEPENDS=	yes
 GNU_CONFIGURE=	yes
 SUB_FILES=	pkg-message
-SHEBANG_FILES=	misc/*.pl misc/plot-bamstats test/test.pl
+SHEBANG_FILES=	misc/*.pl misc/*.py misc/plot-bamstats test/test.pl
 
 CPPFLAGS+=	-I${LOCALBASE}/include
 LDFLAGS+=	-L${LOCALBASE}/lib
 
-MAKE_ENV=	INSTALL_LIB="${INSTALL_LIB}" \
-		INSTALL_DATA="${INSTALL_DATA}" \
-		INSTALL_PROGRAM="${INSTALL_PROGRAM}" \
-		INSTALL_SCRIPT="${INSTALL_SCRIPT}" \
-		INSTALL_DIR="${MKDIR}"
-
-PLIST_SUB=	PORTVERSION="${PORTVERSION}"
-
 TEST_TARGET=	test
-
-post-patch:
-	@${REINPLACE_CMD} -e 's|@PORTVERSION@|${PORTVERSION}|g' ${WRKSRC}/configure.ac
-	${CP} ${FILESDIR}/ax_with_htslib.m4 ${WRKSRC}/
-	${CP} ${FILESDIR}/ax_with_curses.m4 ${WRKSRC}/
 
 .include <bsd.port.mk>

Modified: head/biology/samtools/distinfo
==============================================================================
--- head/biology/samtools/distinfo	Wed Oct 25 10:12:26 2017	(r452839)
+++ head/biology/samtools/distinfo	Wed Oct 25 10:19:50 2017	(r452840)
@@ -1,3 +1,3 @@
-TIMESTAMP = 1463691050
-SHA256 (samtools-samtools-1.3.1_GH0.tar.gz) = 30752c7b92cd9e146f4017983b2a41beb58c8966e93572cea76a14719f95a768
-SIZE (samtools-samtools-1.3.1_GH0.tar.gz) = 3757176
+TIMESTAMP = 1508304738
+SHA256 (samtools-samtools-1.6_GH0.tar.gz) = c0d1ffefe441297ee0eec0e032ac3131519f82fd1a11d38fbcec19e2d5822b28
+SIZE (samtools-samtools-1.6_GH0.tar.gz) = 4014195

Modified: head/biology/samtools/files/patch-Makefile
==============================================================================
--- head/biology/samtools/files/patch-Makefile	Wed Oct 25 10:12:26 2017	(r452839)
+++ head/biology/samtools/files/patch-Makefile	Wed Oct 25 10:19:50 2017	(r452840)
@@ -1,11 +1,11 @@
---- Makefile.orig	2016-04-22 09:22:44 UTC
+--- Makefile.orig	2017-09-28 11:12:01 UTC
 +++ Makefile
-@@ -38,18 +38,18 @@ AOBJS=      bam_index.o bam_plcmd.o sam_
+@@ -40,23 +40,22 @@ 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
+             bam_quickcheck.o bam_addrprg.o bam_markdup.o
  
 -prefix      = /usr/local
-+prefix      = ${STAGEDIR}${PREFIX}
++prefix      = ${PREFIX}
  exec_prefix = $(prefix)
  bindir      = $(exec_prefix)/bin
  datarootdir = $(prefix)/share
@@ -13,46 +13,22 @@
 +mandir      = $(prefix)/man
  man1dir     = $(mandir)/man1
  
--MKDIR_P = mkdir -p
+ # Installation location for $(MISC_PROGRAMS) and $(MISC_SCRIPTS)
+-misc_bindir = $(bindir)
++misc_bindir = $(bindir)/samtools_misc
+ 
+ MKDIR_P = mkdir -p
 -INSTALL = install -p
--INSTALL_PROGRAM = $(INSTALL)
 -INSTALL_DATA    = $(INSTALL) -m 644
 -INSTALL_DIR     = $(MKDIR_P) -m 755
-+#MKDIR_P = mkdir -p
-+#INSTALL = install -p
-+#INSTALL_PROGRAM = $(INSTALL)
-+#INSTALL_DATA    = $(INSTALL) -m 644
-+#INSTALL_DIR     = $(MKDIR_P) -m 755
+-INSTALL_MAN     = $(INSTALL_DATA)
+-INSTALL_PROGRAM = $(INSTALL)
+-INSTALL_SCRIPT  = $(INSTALL_PROGRAM)
++INSTALL_DATA    = ${BSD_INSTALL_DATA}
++INSTALL_DIR     = $(MKDIR_P)
++INSTALL_MAN     = ${BSD_INSTALL_MAN}
++INSTALL_PROGRAM = ${BSD_INSTALL_PROGRAM}
++INSTALL_SCRIPT  = ${BSD_INSTALL_SCRIPT}
  
  
  PROGRAMS = samtools
-@@ -59,7 +59,6 @@ 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 +81,7 @@ 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.
-@@ -280,8 +279,10 @@ 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_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(bindir)/samtools_misc $(DESTDIR)$(man1dir) 
-+	$(INSTALL_PROGRAM) $(PROGRAMS) $(DESTDIR)$(bindir)
-+	$(INSTALL_PROGRAM) $(BUILT_MISC_PROGRAMS) $(DESTDIR)$(bindir)/samtools_misc
-+	$(INSTALL_SCRIPT) $(MISC_PROGRAMS) $(DESTDIR)$(bindir)/samtools_misc
- 	$(INSTALL_DATA) samtools.1 misc/wgsim.1 $(DESTDIR)$(man1dir)
- 
- 

Modified: head/biology/samtools/files/patch-test_test.pl
==============================================================================
--- head/biology/samtools/files/patch-test_test.pl	Wed Oct 25 10:12:26 2017	(r452839)
+++ head/biology/samtools/files/patch-test_test.pl	Wed Oct 25 10:19:50 2017	(r452840)
@@ -1,15 +1,6 @@
---- test/test.pl.orig	2015-12-22 22:43:15 UTC
+--- test/test.pl.orig	2017-10-18 06:08:39 UTC
 +++ test/test.pl
-@@ -136,7 +136,7 @@ sub _cmd
-     else
-     {
-         # child
--        exec('/bin/bash', '-o','pipefail','-c', "($cmd) 2> $err_filename") or error("Cannot execute the command [/bin/sh -o pipefail -c $cmd]: $!");
-+        exec('/usr/local/bin/bash', '-o','pipefail','-c', "($cmd) 2> $err_filename") or error("Cannot execute the command [/usr/local/bin/bash -o pipefail -c $cmd]: $!");
-     }
- }
- sub cmd
-@@ -560,7 +560,7 @@ sub test_usage
+@@ -636,7 +636,7 @@ sub test_usage
      my $command = $args{cmd};
      my $commandpath = $$opts{bin}."/".$command;
      my ($ret,$out,$err) = _cmd("$commandpath $args{redirection}");
@@ -18,7 +9,7 @@
  
      my @sections = ($err =~ m/(^[A-Za-z]+.*?)(?:(?=^[A-Za-z]+:)|\z)/msg);
  
-@@ -615,7 +615,7 @@ sub test_usage_subcommand
+@@ -694,7 +694,7 @@ sub test_usage_subcommand
      my $commandpath = $$opts{bin}."/".$command;
      my ($ret,$out,$err) = _cmd("$commandpath $subcommand $args{redirection}");
  

Modified: head/biology/samtools/files/pkg-message.in
==============================================================================
--- head/biology/samtools/files/pkg-message.in	Wed Oct 25 10:12:26 2017	(r452839)
+++ head/biology/samtools/files/pkg-message.in	Wed Oct 25 10:19:50 2017	(r452840)
@@ -3,5 +3,5 @@ The miscellaneous tools included with Samtools have be
 
 Add that directory to your path if you want to use these tools.
 
-Some of these tools depend on Perl5, and it will need to be installed to
+Some of these tools depend on Perl5/Python, and it will need to be installed to
 use them.



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