biology/{bcftools,htslib,samtools}: update 1.2.x -> 1.3

- Update ports to 1.3 and set BUILD_DEPENDS of dependent ports to require
  version 1.3 of htslib.
- Add CURL option to htslib
- Add TEST_TARGET with perl and bash dependencies for testing
- Tidy up spacing and pkg-message's

PR:		205524
PR:		205525
PR:		205526
Submitted by:	cartwright@asu.edu (maintainer)

9 files changed, 108 insertions, 78 deletions

diff --git a/biology/bcftools/Makefile b/biology/bcftools/Makefile
index c975da132524..ff969014a35e 100644
--- a/biology/bcftools/Makefile
+++ b/biology/bcftools/Makefile
@@ -2,7 +2,7 @@
 # $FreeBSD$
 
 PORTNAME=	bcftools
-PORTVERSION=	1.2
+PORTVERSION=	1.3
 CATEGORIES=	biology
 
 MAINTAINER=	cartwright@asu.edu
@@ -11,15 +11,17 @@ COMMENT=	Tools for manipulating next-generation sequencing data
 LICENSE=	MIT
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
-BUILD_DEPENDS=	htslib>=1.2:${PORTSDIR}/biology/htslib
+BUILD_DEPENDS=	htslib>=1.3:${PORTSDIR}/biology/htslib
 LIB_DEPENDS=	libhts.so:${PORTSDIR}/biology/htslib
+TEST_DEPENDS=	bash:${PORTSDIR}/shells/bash
 
 USE_GITHUB=	yes
 GH_ACCOUNT=	samtools
 
-USES=		gmake shebangfix
+USES=		gmake perl5 shebangfix
+USE_PERL5=	test
 SUB_FILES=	pkg-message
-SHEBANG_FILES=	vcfutils.pl
+SHEBANG_FILES=	vcfutils.pl plot-vcfstats plugins/color-chrs.pl test/test.pl
 
 OPTIONS_DEFINE=	GPL
 GPL_DESC=	Enable modules that rely on GPL code
@@ -33,10 +35,10 @@ 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="${MKDIR}"
+		INSTALL_DATA="${INSTALL_DATA}" \
+		INSTALL_PROGRAM="${INSTALL_PROGRAM}" \
+		INSTALL_SCRIPT="${INSTALL_SCRIPT}" \
+		INSTALL_DIR="${MKDIR}"
 
 .if ${PORT_OPTIONS:MGPL}
 MAKE_ENV+=	USE_GPL=1
@@ -45,4 +47,6 @@ LICENSE=	GPLv3
 
 PLIST_SUB=	PORTVERSION="${PORTVERSION}"
 
+TEST_TARGET=	test
+
 .include <bsd.port.mk>
diff --git a/biology/bcftools/distinfo b/biology/bcftools/distinfo
index 6a97be056ff3..dd518aea8303 100644
--- a/biology/bcftools/distinfo
+++ b/biology/bcftools/distinfo
@@ -1,2 +1,2 @@
-SHA256 (samtools-bcftools-1.2_GH0.tar.gz) = 90ccd7dccfb0b2848b71f32fff073c420260e857b7feeb89c1fb4bfaba49bfba
-SIZE (samtools-bcftools-1.2_GH0.tar.gz) = 511625
+SHA256 (samtools-bcftools-1.3_GH0.tar.gz) = 3f4d4bf68637070cb7dbb5d5619ece7e3315727e651eab751d849085439b11d8
+SIZE (samtools-bcftools-1.3_GH0.tar.gz) = 943041
diff --git a/biology/bcftools/files/patch-Makefile b/biology/bcftools/files/patch-Makefile
index a0bf28174b0f..1d241001fd52 100644
--- a/biology/bcftools/files/patch-Makefile
+++ b/biology/bcftools/files/patch-Makefile
@@ -1,84 +1,78 @@
---- Makefile.orig	2015-02-02 15:40:17 UTC
+--- Makefile.orig	2015-12-15 21:42:34 UTC
 +++ Makefile
-@@ -29,14 +29,13 @@ TEST_PROG=  test/test-rbuf
+@@ -29,16 +29,15 @@ TEST_PROG=  test/test-rbuf
  all: $(PROG) $(TEST_PROG)
  
  # 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)/bgzip
- TABIX  = $(HTSDIR)/tabix
++BGZIP  = $(HTSDIR)/../bin/bgzip
++TABIX  = $(HTSDIR)/../bin/tabix
  
 -CC       = gcc
+-CPPFLAGS =
 -CFLAGS   = -g -Wall -Wc++-compat -O2
-+CC      ?= cc
-+CFLAGS  += -Wall
- DFLAGS   =
+-LDFLAGS  =
++CC       ?= cc
++CPPFLAGS +=
++CFLAGS   += -Wall
++LDFLAGS  +=
+ LIBS     =
+ 
  OBJS     = main.o vcfindex.o tabix.o \
-            vcfstats.o vcfisec.o vcfmerge.o vcfquery.o vcffilter.o filter.o vcfsom.o \
-@@ -52,22 +51,15 @@ INCLUDES = -I. -I$(HTSDIR)
+@@ -57,26 +56,20 @@ GSL_LIBS       =
  ifdef USE_GPL
-     CFLAGS += -DUSE_GPL
-     OBJS   += polysomy.o
--    LDLIBS  = -lgsl -lcblas
-+    LDLIBS += -lgsl -lgslcblas
+     EXTRA_CPPFLAGS += -DUSE_GPL
+     OBJS += polysomy.o peakfit.o
+-    GSL_LIBS = -lgsl -lcblas
++    GSL_LIBS = -lgsl -lgslcblas
  endif
  
 -prefix      = /usr/local
 +prefix      = ${STAGEDIR}${PREFIX}
  exec_prefix = $(prefix)
  bindir      = $(exec_prefix)/bin
+ libdir      = $(exec_prefix)/lib
+ libexecdir  = $(exec_prefix)/libexec
 -mandir      = $(prefix)/share/man
 +mandir      = $(prefix)/man
  man1dir     = $(mandir)/man1
  
+ plugindir   = $(libexecdir)/bcftools
+ pluginpath  = $(plugindir)
+ 
 -MKDIR_P = mkdir -p
 -INSTALL = install -p
 -INSTALL_PROGRAM = $(INSTALL)
 -INSTALL_DATA    = $(INSTALL) -m 644
 -INSTALL_DIR     = $(MKDIR_P) -m 755
 -
--
- all:$(PROG) plugins
- 
- # See htslib/Makefile
-@@ -102,8 +94,8 @@ PLUGINC = $(foreach dir, plugins, $(wild
- PLUGINS = $(PLUGINC:.c=.so)
- PLUGINM = $(PLUGINC:.c=.mk)
+ MISC_PROGRAMS = plot-vcfstats vcfutils.pl plugins/color-chrs.pl
  
--%.so: %.c version.h version.c $(HTSDIR)/libhts.so
--	$(CC) $(CFLAGS) $(INCLUDES) -fPIC -shared -o $@ version.c $< -L$(HTSDIR) -lhts
-+%.so: %.c version.h version.c
-+	$(CC) $(CFLAGS) $(LDFLAGS) $(INCLUDES) -fPIC -shared -o $@ version.c $<  -lhts
- 
- -include $(PLUGINM)
- 
-@@ -156,10 +148,10 @@ version.o: version.h version.c
- test/test-rbuf.o: test/test-rbuf.c rbuf.h
- 
- test/test-rbuf: test/test-rbuf.o
--	$(CC) $(CFLAGS) -o $@ -lm -ldl $<
-+	$(CC) $(CFLAGS) -o $@ -lm $<
+ all:$(PROG) plugins
+@@ -181,7 +174,7 @@ test/test-rbuf: test/test-rbuf.o
+ 	$(CC) $(LDFLAGS) -o $@ $^ -lm $(LIBS)
  
--bcftools: $(HTSLIB) $(OBJS)
--	$(CC) $(CFLAGS) -o $@ $(OBJS) $(HTSLIB) -lpthread -lz -lm -ldl $(LDLIBS)
-+bcftools: $(OBJS)
-+	$(CC) -pthread $(CFLAGS) $(LDFLAGS) -o $@ $(OBJS) $(HTSLIB)  -lz -lm $(LDLIBS)
+ 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)
  
  doc/bcftools.1: doc/bcftools.txt
  	cd doc && a2x -adate="$(DOC_DATE)" -aversion=$(DOC_VERSION) --doctype manpage --format manpage bcftools.txt
-@@ -170,8 +162,9 @@ doc/bcftools.html: doc/bcftools.txt
- docs: doc/bcftools.1 doc/bcftools.html
- 
- install: $(PROG) doc/bcftools.1
--	$(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(man1dir)
--	$(INSTALL_PROGRAM) $(PROG) plot-vcfstats vcfutils.pl $(DESTDIR)$(bindir)
-+	$(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(bindir)/samtools_misc $(DESTDIR)$(man1dir)
+@@ -198,8 +191,9 @@ 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_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) plot-vcfstats vcfutils.pl $(DESTDIR)$(bindir)/samtools_misc
++	$(INSTALL_SCRIPT) $(MISC_PROGRAMS) $(DESTDIR)$(bindir)/samtools_misc
  	$(INSTALL_DATA) doc/bcftools.1 $(DESTDIR)$(man1dir)
+ 	$(INSTALL_PROGRAM) plugins/*.so $(DESTDIR)$(plugindir)
  
- clean: testclean clean-plugins
diff --git a/biology/bcftools/files/patch-plugins_fixploidy.mk b/biology/bcftools/files/patch-plugins_fixploidy.mk
deleted file mode 100644
index 909de819997d..000000000000
--- a/biology/bcftools/files/patch-plugins_fixploidy.mk
+++ /dev/null
@@ -1,7 +0,0 @@
---- plugins/fixploidy.mk.orig	2015-02-02 15:40:17 UTC
-+++ plugins/fixploidy.mk
-@@ -1,2 +1,2 @@
--plugins/fixploidy.so: plugins/fixploidy.c version.h version.c ploidy.h ploidy.c $(HTSDIR)/libhts.so
--	$(CC) $(CFLAGS) $(INCLUDES) -fPIC -shared -o $@ ploidy.c version.c $< -L$(HTSDIR) -lhts
-+plugins/fixploidy.so: plugins/fixploidy.c version.h version.c ploidy.h ploidy.c
-+	$(CC) $(CFLAGS) $(LDFLAGS) $(INCLUDES) -fPIC -shared -o $@ ploidy.c version.c $< -lhts
diff --git a/biology/bcftools/files/patch-plugins_vcf2sex.mk b/biology/bcftools/files/patch-plugins_vcf2sex.mk
deleted file mode 100644
index 15619f0661db..000000000000
--- a/biology/bcftools/files/patch-plugins_vcf2sex.mk
+++ /dev/null
@@ -1,7 +0,0 @@
---- plugins/vcf2sex.mk.orig	2015-02-02 15:40:17 UTC
-+++ plugins/vcf2sex.mk
-@@ -1,2 +1,2 @@
--plugins/vcf2sex.so: plugins/vcf2sex.c version.h version.c ploidy.h ploidy.c $(HTSDIR)/libhts.so
--	$(CC) $(CFLAGS) $(INCLUDES) -fPIC -shared -o $@ ploidy.c version.c $< -L$(HTSDIR) -lhts
-+plugins/vcf2sex.so: plugins/vcf2sex.c version.h version.c ploidy.h ploidy.c
-+	$(CC) $(CFLAGS) $(LDFLAGS) $(INCLUDES) -fPIC -shared -o $@ ploidy.c version.c $< -lhts
diff --git a/biology/bcftools/files/patch-prob1.c b/biology/bcftools/files/patch-prob1.c
index 334d1bd37e23..04694984b8c8 100644
--- a/biology/bcftools/files/patch-prob1.c
+++ b/biology/bcftools/files/patch-prob1.c
@@ -1,15 +1,13 @@
---- prob1.c.orig	2015-04-28 01:28:23 UTC
+--- prob1.c.orig	2015-12-15 21:42:34 UTC
 +++ prob1.c
-@@ -33,6 +33,14 @@ THE SOFTWARE.  */
+@@ -33,6 +33,12 @@ THE SOFTWARE.  */
  #include <zlib.h>
  #include "prob1.h"
  
 +#include <sys/param.h>
-+#ifdef __FreeBSD__
-+#	if __FreeBSD_version < 1000034
-+#		define logl(x) log(x)
-+#		define expl(x) exp(x)
-+#	endif
++#if defined(__FreeBSD__) && (__FreeBSD_version < 1000034)
++#	define logl(x) log(x)
++#	define expl(x) exp(x)
 +#endif
 +
  // #include "kstring.h"
diff --git a/biology/bcftools/files/patch-test_test.pl b/biology/bcftools/files/patch-test_test.pl
new file mode 100644
index 000000000000..e5c436a3775a
--- /dev/null
+++ b/biology/bcftools/files/patch-test_test.pl
@@ -0,0 +1,29 @@
+--- test/test.pl.orig	2015-12-22 22:45:13 UTC
++++ test/test.pl
+@@ -290,7 +290,7 @@ sub _cmd
+     else
+     {
+         # child
+-        exec('/bin/bash', '-o','pipefail','-c', $cmd) or error("Cannot execute the command [/bin/sh -o pipefail -c $cmd]: $!");
++        exec('/usr/local/bin/bash', '-o','pipefail','-c', $cmd) or error("Cannot execute the command [/usr/local/bin/sh -o pipefail -c $cmd]: $!");
+     }
+     return ($? >> 8, join('',@out));
+ }
+@@ -657,7 +657,7 @@ sub test_usage
+     my $command = $args{cmd};
+     my $commandpath = $$opts{bin}."/".$command;
+     my ($ret,$out) = _cmd("$commandpath $args{redirection} 2>&1");
+-    if ( $out =~ m/\/bin\/bash.*no.*such/i ) { failed($opts,$test,"could not run $commandpath: $out"); return; }
++    if ( $out =~ m/\/usr\/local\/bin\/bash.*no.*such/i ) { failed($opts,$test,"could not run $commandpath: $out"); return; }
+ 
+     my @sections = ($out =~ m/(^[A-Za-z]+.*?)(?:(?=^[A-Za-z]+:)|\z)/msg);
+ 
+@@ -708,7 +708,7 @@ sub test_usage_subcommand
+     my $subcommand = $args{subcmd};
+     my $commandpath = $$opts{bin}."/".$command;
+     my ($ret,$out) = _cmd("$commandpath $subcommand $args{redirection} 2>&1");
+-    if ( $out =~ m/\/bin\/bash.*no.*such/i ) { failed($opts,$test,"could not run $commandpath $subcommand: $out"); return; }
++    if ( $out =~ m/\/usr\/local\/bin\/bash.*no.*such/i ) { failed($opts,$test,"could not run $commandpath $subcommand: $out"); return; }
+ 
+     my @sections = ($out =~ m/(^[A-Za-z]+.*?)(?:(?=^[A-Za-z]+:)|\z)/msg);
+ 
diff --git a/biology/bcftools/files/pkg-message.in b/biology/bcftools/files/pkg-message.in
index 27c8cb9c4c51..fde8ffcdab72 100644
--- a/biology/bcftools/files/pkg-message.in
+++ b/biology/bcftools/files/pkg-message.in
@@ -1,2 +1,7 @@
+The miscellaneous tools included with Bcftools have been installed to
+%%PREFIX%%/bin/samtools_misc 
 
-Add %%PREFIX%%/bin/samtools_misc to your path to use miscellaneous tools.
+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
+use them.
diff --git a/biology/bcftools/pkg-plist b/biology/bcftools/pkg-plist
index 0098a1c9afb0..46544ca50e9f 100644
--- a/biology/bcftools/pkg-plist
+++ b/biology/bcftools/pkg-plist
@@ -1,4 +1,18 @@
 bin/bcftools
+bin/samtools_misc/color-chrs.pl
 bin/samtools_misc/plot-vcfstats
 bin/samtools_misc/vcfutils.pl
+libexec/bcftools/color-chrs.so
+libexec/bcftools/counts.so
+libexec/bcftools/dosage.so
+libexec/bcftools/fill-AN-AC.so
+libexec/bcftools/fill-tags.so
+libexec/bcftools/fixploidy.so
+libexec/bcftools/frameshifts.so
+libexec/bcftools/impute-info.so
+libexec/bcftools/mendelian.so
+libexec/bcftools/missing2ref.so
+libexec/bcftools/setGT.so
+libexec/bcftools/tag2tag.so
+libexec/bcftools/vcf2sex.so
 man/man1/bcftools.1.gz