Index: Makefile
===================================================================
--- Makefile	(revision 452329)
+++ Makefile	(working copy)
@@ -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 @@
 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 @@
 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 @@
 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>
Index: distinfo
===================================================================
--- distinfo	(revision 452329)
+++ distinfo	(working copy)
@@ -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
Index: files/patch-Makefile
===================================================================
--- files/patch-Makefile	(revision 452329)
+++ files/patch-Makefile	(working copy)
@@ -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)
Index: files/patch-configure.ac
===================================================================
--- files/patch-configure.ac	(revision 0)
+++ files/patch-configure.ac	(working copy)
@@ -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])

Property changes on: files/patch-configure.ac
___________________________________________________________________
Added: fbsd:nokeywords
## -0,0 +1 ##
+yes
\ No newline at end of property
Added: svn:eol-style
## -0,0 +1 ##
+native
\ No newline at end of property
Added: svn:mime-type
## -0,0 +1 ##
+text/plain
\ No newline at end of property
Index: files/patch-misc_run-roh.pl
===================================================================
--- files/patch-misc_run-roh.pl	(revision 0)
+++ files/patch-misc_run-roh.pl	(working copy)
@@ -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; }

Property changes on: files/patch-misc_run-roh.pl
___________________________________________________________________
Added: fbsd:nokeywords
## -0,0 +1 ##
+yes
\ No newline at end of property
Added: svn:eol-style
## -0,0 +1 ##
+native
\ No newline at end of property
Added: svn:mime-type
## -0,0 +1 ##
+text/plain
\ No newline at end of property
Index: files/patch-prob1.c
===================================================================
--- files/patch-prob1.c	(revision 452329)
+++ files/patch-prob1.c	(working copy)
@@ -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>
Index: files/patch-test_test.pl
===================================================================
--- files/patch-test_test.pl	(revision 452329)
+++ files/patch-test_test.pl	(working copy)
@@ -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");
Index: files/pkg-message.in
===================================================================
--- files/pkg-message.in	(revision 452329)
+++ files/pkg-message.in	(working copy)
@@ -3,5 +3,5 @@
 
 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.
Index: pkg-plist
===================================================================
--- pkg-plist	(revision 452329)
+++ pkg-plist	(working copy)
@@ -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