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Index: head/biology/bcftools/Makefile
===================================================================
--- head/biology/bcftools/Makefile
+++ head/biology/bcftools/Makefile
@@ -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: head/biology/bcftools/distinfo
===================================================================
--- head/biology/bcftools/distinfo
+++ head/biology/bcftools/distinfo
@@ -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: head/biology/bcftools/files/patch-Makefile
===================================================================
--- head/biology/bcftools/files/patch-Makefile
+++ head/biology/bcftools/files/patch-Makefile
@@ -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: head/biology/bcftools/files/patch-configure.ac
===================================================================
--- head/biology/bcftools/files/patch-configure.ac
+++ head/biology/bcftools/files/patch-configure.ac
@@ -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])
Index: head/biology/bcftools/files/patch-misc_run-roh.pl
===================================================================
--- head/biology/bcftools/files/patch-misc_run-roh.pl
+++ head/biology/bcftools/files/patch-misc_run-roh.pl
@@ -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}) && !$args{exit_on_error} ) { return @out; }
Index: head/biology/bcftools/files/patch-prob1.c
===================================================================
--- head/biology/bcftools/files/patch-prob1.c
+++ head/biology/bcftools/files/patch-prob1.c
@@ -1,4 +1,4 @@
---- prob1.c.orig 2015-12-15 21:42:34 UTC
+--- prob1.c.orig 2017-09-28 11:22:48 UTC
+++ prob1.c
@@ -33,6 +33,12 @@ THE SOFTWARE. */
#include <zlib.h>
Index: head/biology/bcftools/files/patch-test_test.pl
===================================================================
--- head/biology/bcftools/files/patch-test_test.pl
+++ head/biology/bcftools/files/patch-test_test.pl
@@ -1,6 +1,6 @@
---- test/test.pl.orig 2015-12-22 22:45:13 UTC
+--- test/test.pl.orig 2017-10-18 09:33:24 UTC
+++ test/test.pl
-@@ -290,7 +290,7 @@ sub _cmd
+@@ -381,7 +381,7 @@ sub _cmd
else
{
# child
@@ -9,7 +9,7 @@
}
return ($? >> 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: head/biology/bcftools/files/pkg-message.in
===================================================================
--- head/biology/bcftools/files/pkg-message.in
+++ head/biology/bcftools/files/pkg-message.in
@@ -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: head/biology/bcftools/pkg-plist
===================================================================
--- head/biology/bcftools/pkg-plist
+++ head/biology/bcftools/pkg-plist
@@ -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
Index: head/biology/htslib/Makefile
===================================================================
--- head/biology/htslib/Makefile
+++ head/biology/htslib/Makefile
@@ -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 @@
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>
Index: head/biology/htslib/distinfo
===================================================================
--- head/biology/htslib/distinfo
+++ head/biology/htslib/distinfo
@@ -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
Index: head/biology/htslib/files/patch-Makefile
===================================================================
--- head/biology/htslib/files/patch-Makefile
+++ head/biology/htslib/files/patch-Makefile
@@ -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)
-
Index: head/biology/htslib/files/patch-configure.ac
===================================================================
--- head/biology/htslib/files/patch-configure.ac
+++ head/biology/htslib/files/patch-configure.ac
@@ -1,11 +0,0 @@
---- configure.ac.orig 2015-12-15 16:34:33 UTC
-+++ configure.ac
-@@ -23,7 +23,7 @@
- # DEALINGS IN THE SOFTWARE.
-
- dnl Process this file with autoconf to produce a configure script
--AC_INIT([HTSlib], m4_esyscmd_s([make print-version]),
-+AC_INIT([HTSlib], [1.3],
- [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(hts.c)
Index: head/biology/htslib/files/patch-hfile__libcurl.c
===================================================================
--- head/biology/htslib/files/patch-hfile__libcurl.c
+++ head/biology/htslib/files/patch-hfile__libcurl.c
@@ -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
Index: head/biology/htslib/pkg-plist
===================================================================
--- head/biology/htslib/pkg-plist
+++ head/biology/htslib/pkg-plist
@@ -7,6 +7,9 @@
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/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
Index: head/biology/samtools/Makefile
===================================================================
--- head/biology/samtools/Makefile
+++ head/biology/samtools/Makefile
@@ -2,7 +2,7 @@
# $FreeBSD$
PORTNAME= samtools
-PORTVERSION= 1.3.1
+PORTVERSION= 1.6
CATEGORIES= biology
MAINTAINER= cartwright@asu.edu
@@ -11,34 +11,22 @@
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>
Index: head/biology/samtools/distinfo
===================================================================
--- head/biology/samtools/distinfo
+++ head/biology/samtools/distinfo
@@ -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
Index: head/biology/samtools/files/ax_with_curses.m4
===================================================================
--- head/biology/samtools/files/ax_with_curses.m4
+++ head/biology/samtools/files/ax_with_curses.m4
@@ -1,518 +0,0 @@
-# ===========================================================================
-# http://www.gnu.org/software/autoconf-archive/ax_with_curses.html
-# ===========================================================================
-#
-# SYNOPSIS
-#
-# AX_WITH_CURSES
-#
-# DESCRIPTION
-#
-# This macro checks whether a SysV or X/Open-compatible Curses library is
-# present, along with the associated header file. The NcursesW
-# (wide-character) library is searched for first, followed by Ncurses,
-# then the system-default plain Curses. The first library found is the
-# one returned.
-#
-# The following options are understood: --with-ncursesw, --with-ncurses,
-# --without-ncursesw, --without-ncurses. The "--with" options force the
-# macro to use that particular library, terminating with an error if not
-# found. The "--without" options simply skip the check for that library.
-# The effect on the search pattern is:
-#
-# (no options) - NcursesW, Ncurses, Curses
-# --with-ncurses --with-ncursesw - NcursesW only [*]
-# --without-ncurses --with-ncursesw - NcursesW only [*]
-# --with-ncursesw - NcursesW only [*]
-# --with-ncurses --without-ncursesw - Ncurses only [*]
-# --with-ncurses - NcursesW, Ncurses [**]
-# --without-ncurses --without-ncursesw - Curses only
-# --without-ncursesw - Ncurses, Curses
-# --without-ncurses - NcursesW, Curses
-#
-# [*] If the library is not found, abort the configure script.
-#
-# [**] If the second library (Ncurses) is not found, abort configure.
-#
-# The following preprocessor symbols may be defined by this macro if the
-# appropriate conditions are met:
-#
-# HAVE_CURSES - if any SysV or X/Open Curses library found
-# HAVE_CURSES_ENHANCED - if library supports X/Open Enhanced functions
-# HAVE_CURSES_COLOR - if library supports color (enhanced functions)
-# HAVE_CURSES_OBSOLETE - if library supports certain obsolete features
-# HAVE_NCURSESW - if NcursesW (wide char) library is to be used
-# HAVE_NCURSES - if the Ncurses library is to be used
-#
-# HAVE_CURSES_H - if <curses.h> is present and should be used
-# HAVE_NCURSESW_H - if <ncursesw.h> should be used
-# HAVE_NCURSES_H - if <ncurses.h> should be used
-# HAVE_NCURSESW_CURSES_H - if <ncursesw/curses.h> should be used
-# HAVE_NCURSES_CURSES_H - if <ncurses/curses.h> should be used
-#
-# (These preprocessor symbols are discussed later in this document.)
-#
-# The following output variable is defined by this macro; it is precious
-# and may be overridden on the ./configure command line:
-#
-# CURSES_LIB - library to add to xxx_LDADD
-#
-# The library listed in CURSES_LIB is NOT added to LIBS by default. You
-# need to add CURSES_LIB to the appropriate xxx_LDADD line in your
-# Makefile.am. For example:
-#
-# prog_LDADD = @CURSES_LIB@
-#
-# If CURSES_LIB is set on the configure command line (such as by running
-# "./configure CURSES_LIB=-lmycurses"), then the only header searched for
-# is <curses.h>. The user may use the CPPFLAGS precious variable to
-# override the standard #include search path. If the user needs to
-# specify an alternative path for a library (such as for a non-standard
-# NcurseW), the user should use the LDFLAGS variable.
-#
-# The following shell variables may be defined by this macro:
-#
-# ax_cv_curses - set to "yes" if any Curses library found
-# ax_cv_curses_enhanced - set to "yes" if Enhanced functions present
-# ax_cv_curses_color - set to "yes" if color functions present
-# ax_cv_curses_obsolete - set to "yes" if obsolete features present
-#
-# ax_cv_ncursesw - set to "yes" if NcursesW library found
-# ax_cv_ncurses - set to "yes" if Ncurses library found
-# ax_cv_plaincurses - set to "yes" if plain Curses library found
-# ax_cv_curses_which - set to "ncursesw", "ncurses", "plaincurses" or "no"
-#
-# These variables can be used in your configure.ac to determine the level
-# of support you need from the Curses library. For example, if you must
-# have either Ncurses or NcursesW, you could include:
-#
-# AX_WITH_CURSES
-# if test "x$ax_cv_ncursesw" != xyes && test "x$ax_cv_ncurses" != xyes; then
-# AC_MSG_ERROR([requires either NcursesW or Ncurses library])
-# fi
-#
-# If any Curses library will do (but one must be present and must support
-# color), you could use:
-#
-# AX_WITH_CURSES
-# if test "x$ax_cv_curses" != xyes || test "x$ax_cv_curses_color" != xyes; then
-# AC_MSG_ERROR([requires an X/Open-compatible Curses library with color])
-# fi
-#
-# Certain preprocessor symbols and shell variables defined by this macro
-# can be used to determine various features of the Curses library. In
-# particular, HAVE_CURSES and ax_cv_curses are defined if the Curses
-# library found conforms to the traditional SysV and/or X/Open Base Curses
-# definition. Any working Curses library conforms to this level.
-#
-# HAVE_CURSES_ENHANCED and ax_cv_curses_enhanced are defined if the
-# library supports the X/Open Enhanced Curses definition. In particular,
-# the wide-character types attr_t, cchar_t and wint_t, the functions
-# wattr_set() and wget_wch() and the macros WA_NORMAL and _XOPEN_CURSES
-# are checked. The Ncurses library does NOT conform to this definition,
-# although NcursesW does.
-#
-# HAVE_CURSES_COLOR and ax_cv_curses_color are defined if the library
-# supports color functions and macros such as COLOR_PAIR, A_COLOR,
-# COLOR_WHITE, COLOR_RED and init_pair(). These are NOT part of the
-# X/Open Base Curses definition, but are part of the Enhanced set of
-# functions. The Ncurses library DOES support these functions, as does
-# NcursesW.
-#
-# HAVE_CURSES_OBSOLETE and ax_cv_curses_obsolete are defined if the
-# library supports certain features present in SysV and BSD Curses but not
-# defined in the X/Open definition. In particular, the functions
-# getattrs(), getcurx() and getmaxx() are checked.
-#
-# To use the HAVE_xxx_H preprocessor symbols, insert the following into
-# your system.h (or equivalent) header file:
-#
-# #if defined HAVE_NCURSESW_CURSES_H
-# # include <ncursesw/curses.h>
-# #elif defined HAVE_NCURSESW_H
-# # include <ncursesw.h>
-# #elif defined HAVE_NCURSES_CURSES_H
-# # include <ncurses/curses.h>
-# #elif defined HAVE_NCURSES_H
-# # include <ncurses.h>
-# #elif defined HAVE_CURSES_H
-# # include <curses.h>
-# #else
-# # error "SysV or X/Open-compatible Curses header file required"
-# #endif
-#
-# For previous users of this macro: you should not need to change anything
-# in your configure.ac or Makefile.am, as the previous (serial 10)
-# semantics are still valid. However, you should update your system.h (or
-# equivalent) header file to the fragment shown above. You are encouraged
-# also to make use of the extended functionality provided by this version
-# of AX_WITH_CURSES, as well as in the additional macros
-# AX_WITH_CURSES_PANEL, AX_WITH_CURSES_MENU and AX_WITH_CURSES_FORM.
-#
-# LICENSE
-#
-# Copyright (c) 2009 Mark Pulford <mark@kyne.com.au>
-# Copyright (c) 2009 Damian Pietras <daper@daper.net>
-# Copyright (c) 2012 Reuben Thomas <rrt@sc3d.org>
-# Copyright (c) 2011 John Zaitseff <J.Zaitseff@zap.org.au>
-#
-# This program is free software: you can redistribute it and/or modify it
-# under the terms of the GNU General Public License as published by the
-# Free Software Foundation, either version 3 of the License, or (at your
-# option) any later version.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
-# Public License for more details.
-#
-# You should have received a copy of the GNU General Public License along
-# with this program. If not, see <http://www.gnu.org/licenses/>.
-#
-# As a special exception, the respective Autoconf Macro's copyright owner
-# gives unlimited permission to copy, distribute and modify the configure
-# scripts that are the output of Autoconf when processing the Macro. You
-# need not follow the terms of the GNU General Public License when using
-# or distributing such scripts, even though portions of the text of the
-# Macro appear in them. The GNU General Public License (GPL) does govern
-# all other use of the material that constitutes the Autoconf Macro.
-#
-# This special exception to the GPL applies to versions of the Autoconf
-# Macro released by the Autoconf Archive. When you make and distribute a
-# modified version of the Autoconf Macro, you may extend this special
-# exception to the GPL to apply to your modified version as well.
-
-#serial 15
-
-AU_ALIAS([MP_WITH_CURSES], [AX_WITH_CURSES])
-AC_DEFUN([AX_WITH_CURSES], [
- AC_ARG_VAR([CURSES_LIB], [linker library for Curses, e.g. -lcurses])
- AC_ARG_WITH([ncurses], [AS_HELP_STRING([--with-ncurses],
- [force the use of Ncurses or NcursesW])],
- [], [with_ncurses=check])
- AC_ARG_WITH([ncursesw], [AS_HELP_STRING([--without-ncursesw],
- [do not use NcursesW (wide character support)])],
- [], [with_ncursesw=check])
-
- ax_saved_LIBS=$LIBS
- AS_IF([test "x$with_ncurses" = xyes || test "x$with_ncursesw" = xyes],
- [ax_with_plaincurses=no], [ax_with_plaincurses=check])
-
- ax_cv_curses_which=no
-
- # Test for NcursesW
-
- AS_IF([test "x$CURSES_LIB" = x && test "x$with_ncursesw" != xno], [
- LIBS="$ax_saved_LIBS -lncursesw"
-
- AC_CACHE_CHECK([for NcursesW wide-character library], [ax_cv_ncursesw], [
- AC_LINK_IFELSE([AC_LANG_CALL([], [initscr])],
- [ax_cv_ncursesw=yes], [ax_cv_ncursesw=no])
- ])
- AS_IF([test "x$ax_cv_ncursesw" = xno && test "x$with_ncursesw" = xyes], [
- AC_MSG_ERROR([--with-ncursesw specified but could not find NcursesW library])
- ])
-
- AS_IF([test "x$ax_cv_ncursesw" = xyes], [
- ax_cv_curses=yes
- ax_cv_curses_which=ncursesw
- CURSES_LIB="-lncursesw"
- AC_DEFINE([HAVE_NCURSESW], [1], [Define to 1 if the NcursesW library is present])
- AC_DEFINE([HAVE_CURSES], [1], [Define to 1 if a SysV or X/Open compatible Curses library is present])
-
- AC_CACHE_CHECK([for working ncursesw/curses.h], [ax_cv_header_ncursesw_curses_h], [
- AC_LINK_IFELSE([AC_LANG_PROGRAM([[
- @%:@define _XOPEN_SOURCE_EXTENDED 1
- @%:@include <ncursesw/curses.h>
- ]], [[
- chtype a = A_BOLD;
- int b = KEY_LEFT;
- chtype c = COLOR_PAIR(1) & A_COLOR;
- attr_t d = WA_NORMAL;
- cchar_t e;
- wint_t f;
- int g = getattrs(stdscr);
- int h = getcurx(stdscr) + getmaxx(stdscr);
- initscr();
- init_pair(1, COLOR_WHITE, COLOR_RED);
- wattr_set(stdscr, d, 0, NULL);
- wget_wch(stdscr, &f);
- ]])],
- [ax_cv_header_ncursesw_curses_h=yes],
- [ax_cv_header_ncursesw_curses_h=no])
- ])
- AS_IF([test "x$ax_cv_header_ncursesw_curses_h" = xyes], [
- ax_cv_curses_enhanced=yes
- ax_cv_curses_color=yes
- ax_cv_curses_obsolete=yes
- AC_DEFINE([HAVE_CURSES_ENHANCED], [1], [Define to 1 if library supports X/Open Enhanced functions])
- AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)])
- AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features])
- AC_DEFINE([HAVE_NCURSESW_CURSES_H], [1], [Define to 1 if <ncursesw/curses.h> is present])
- ])
-
- AC_CACHE_CHECK([for working ncursesw.h], [ax_cv_header_ncursesw_h], [
- AC_LINK_IFELSE([AC_LANG_PROGRAM([[
- @%:@define _XOPEN_SOURCE_EXTENDED 1
- @%:@include <ncursesw.h>
- ]], [[
- chtype a = A_BOLD;
- int b = KEY_LEFT;
- chtype c = COLOR_PAIR(1) & A_COLOR;
- attr_t d = WA_NORMAL;
- cchar_t e;
- wint_t f;
- int g = getattrs(stdscr);
- int h = getcurx(stdscr) + getmaxx(stdscr);
- initscr();
- init_pair(1, COLOR_WHITE, COLOR_RED);
- wattr_set(stdscr, d, 0, NULL);
- wget_wch(stdscr, &f);
- ]])],
- [ax_cv_header_ncursesw_h=yes],
- [ax_cv_header_ncursesw_h=no])
- ])
- AS_IF([test "x$ax_cv_header_ncursesw_h" = xyes], [
- ax_cv_curses_enhanced=yes
- ax_cv_curses_color=yes
- ax_cv_curses_obsolete=yes
- AC_DEFINE([HAVE_CURSES_ENHANCED], [1], [Define to 1 if library supports X/Open Enhanced functions])
- AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)])
- AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features])
- AC_DEFINE([HAVE_NCURSESW_H], [1], [Define to 1 if <ncursesw.h> is present])
- ])
-
- AC_CACHE_CHECK([for working ncurses.h], [ax_cv_header_ncurses_h_with_ncursesw], [
- AC_LINK_IFELSE([AC_LANG_PROGRAM([[
- @%:@define _XOPEN_SOURCE_EXTENDED 1
- @%:@include <ncurses.h>
- ]], [[
- chtype a = A_BOLD;
- int b = KEY_LEFT;
- chtype c = COLOR_PAIR(1) & A_COLOR;
- attr_t d = WA_NORMAL;
- cchar_t e;
- wint_t f;
- int g = getattrs(stdscr);
- int h = getcurx(stdscr) + getmaxx(stdscr);
- initscr();
- init_pair(1, COLOR_WHITE, COLOR_RED);
- wattr_set(stdscr, d, 0, NULL);
- wget_wch(stdscr, &f);
- ]])],
- [ax_cv_header_ncurses_h_with_ncursesw=yes],
- [ax_cv_header_ncurses_h_with_ncursesw=no])
- ])
- AS_IF([test "x$ax_cv_header_ncurses_h_with_ncursesw" = xyes], [
- ax_cv_curses_enhanced=yes
- ax_cv_curses_color=yes
- ax_cv_curses_obsolete=yes
- AC_DEFINE([HAVE_CURSES_ENHANCED], [1], [Define to 1 if library supports X/Open Enhanced functions])
- AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)])
- AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features])
- AC_DEFINE([HAVE_NCURSES_H], [1], [Define to 1 if <ncurses.h> is present])
- ])
-
- AS_IF([test "x$ax_cv_header_ncursesw_curses_h" = xno && test "x$ax_cv_header_ncursesw_h" = xno && test "x$ax_cv_header_ncurses_h_with_ncursesw" = xno], [
- AC_MSG_WARN([could not find a working ncursesw/curses.h, ncursesw.h or ncurses.h])
- ])
- ])
- ])
-
- # Test for Ncurses
-
- AS_IF([test "x$CURSES_LIB" = x && test "x$with_ncurses" != xno && test "x$ax_cv_curses_which" = xno], [
- LIBS="$ax_saved_LIBS -lncurses"
-
- AC_CACHE_CHECK([for Ncurses library], [ax_cv_ncurses], [
- AC_LINK_IFELSE([AC_LANG_CALL([], [initscr])],
- [ax_cv_ncurses=yes], [ax_cv_ncurses=no])
- ])
- AS_IF([test "x$ax_cv_ncurses" = xno && test "x$with_ncurses" = xyes], [
- AC_MSG_ERROR([--with-ncurses specified but could not find Ncurses library])
- ])
-
- AS_IF([test "x$ax_cv_ncurses" = xyes], [
- ax_cv_curses=yes
- ax_cv_curses_which=ncurses
- CURSES_LIB="-lncurses"
- AC_DEFINE([HAVE_NCURSES], [1], [Define to 1 if the Ncurses library is present])
- AC_DEFINE([HAVE_CURSES], [1], [Define to 1 if a SysV or X/Open compatible Curses library is present])
-
- AC_CACHE_CHECK([for working ncurses/curses.h], [ax_cv_header_ncurses_curses_h], [
- AC_LINK_IFELSE([AC_LANG_PROGRAM([[
- @%:@include <ncurses/curses.h>
- ]], [[
- chtype a = A_BOLD;
- int b = KEY_LEFT;
- chtype c = COLOR_PAIR(1) & A_COLOR;
- int g = getattrs(stdscr);
- int h = getcurx(stdscr) + getmaxx(stdscr);
- initscr();
- init_pair(1, COLOR_WHITE, COLOR_RED);
- ]])],
- [ax_cv_header_ncurses_curses_h=yes],
- [ax_cv_header_ncurses_curses_h=no])
- ])
- AS_IF([test "x$ax_cv_header_ncurses_curses_h" = xyes], [
- ax_cv_curses_color=yes
- ax_cv_curses_obsolete=yes
- AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)])
- AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features])
- AC_DEFINE([HAVE_NCURSES_CURSES_H], [1], [Define to 1 if <ncurses/curses.h> is present])
- ])
-
- AC_CACHE_CHECK([for working ncurses.h], [ax_cv_header_ncurses_h], [
- AC_LINK_IFELSE([AC_LANG_PROGRAM([[
- @%:@include <ncurses.h>
- ]], [[
- chtype a = A_BOLD;
- int b = KEY_LEFT;
- chtype c = COLOR_PAIR(1) & A_COLOR;
- int g = getattrs(stdscr);
- int h = getcurx(stdscr) + getmaxx(stdscr);
- initscr();
- init_pair(1, COLOR_WHITE, COLOR_RED);
- ]])],
- [ax_cv_header_ncurses_h=yes],
- [ax_cv_header_ncurses_h=no])
- ])
- AS_IF([test "x$ax_cv_header_ncurses_h" = xyes], [
- ax_cv_curses_color=yes
- ax_cv_curses_obsolete=yes
- AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)])
- AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features])
- AC_DEFINE([HAVE_NCURSES_H], [1], [Define to 1 if <ncurses.h> is present])
- ])
-
- AS_IF([test "x$ax_cv_header_ncurses_curses_h" = xno && test "x$ax_cv_header_ncurses_h" = xno], [
- AC_MSG_WARN([could not find a working ncurses/curses.h or ncurses.h])
- ])
- ])
- ])
-
- # Test for plain Curses (or if CURSES_LIB was set by user)
-
- AS_IF([test "x$with_plaincurses" != xno && test "x$ax_cv_curses_which" = xno], [
- AS_IF([test "x$CURSES_LIB" != x], [
- LIBS="$ax_saved_LIBS $CURSES_LIB"
- ], [
- LIBS="$ax_saved_LIBS -lcurses"
- ])
-
- AC_CACHE_CHECK([for Curses library], [ax_cv_plaincurses], [
- AC_LINK_IFELSE([AC_LANG_CALL([], [initscr])],
- [ax_cv_plaincurses=yes], [ax_cv_plaincurses=no])
- ])
-
- AS_IF([test "x$ax_cv_plaincurses" = xyes], [
- ax_cv_curses=yes
- ax_cv_curses_which=plaincurses
- AS_IF([test "x$CURSES_LIB" = x], [
- CURSES_LIB="-lcurses"
- ])
- AC_DEFINE([HAVE_CURSES], [1], [Define to 1 if a SysV or X/Open compatible Curses library is present])
-
- # Check for base conformance (and header file)
-
- AC_CACHE_CHECK([for working curses.h], [ax_cv_header_curses_h], [
- AC_LINK_IFELSE([AC_LANG_PROGRAM([[
- @%:@include <curses.h>
- ]], [[
- chtype a = A_BOLD;
- int b = KEY_LEFT;
- initscr();
- ]])],
- [ax_cv_header_curses_h=yes],
- [ax_cv_header_curses_h=no])
- ])
- AS_IF([test "x$ax_cv_header_curses_h" = xyes], [
- AC_DEFINE([HAVE_CURSES_H], [1], [Define to 1 if <curses.h> is present])
-
- # Check for X/Open Enhanced conformance
-
- AC_CACHE_CHECK([for X/Open Enhanced Curses conformance], [ax_cv_plaincurses_enhanced], [
- AC_LINK_IFELSE([AC_LANG_PROGRAM([[
- @%:@define _XOPEN_SOURCE_EXTENDED 1
- @%:@include <curses.h>
- @%:@ifndef _XOPEN_CURSES
- @%:@error "this Curses library is not enhanced"
- "this Curses library is not enhanced"
- @%:@endif
- ]], [[
- chtype a = A_BOLD;
- int b = KEY_LEFT;
- chtype c = COLOR_PAIR(1) & A_COLOR;
- attr_t d = WA_NORMAL;
- cchar_t e;
- wint_t f;
- initscr();
- init_pair(1, COLOR_WHITE, COLOR_RED);
- wattr_set(stdscr, d, 0, NULL);
- wget_wch(stdscr, &f);
- ]])],
- [ax_cv_plaincurses_enhanced=yes],
- [ax_cv_plaincurses_enhanced=no])
- ])
- AS_IF([test "x$ax_cv_plaincurses_enhanced" = xyes], [
- ax_cv_curses_enhanced=yes
- ax_cv_curses_color=yes
- AC_DEFINE([HAVE_CURSES_ENHANCED], [1], [Define to 1 if library supports X/Open Enhanced functions])
- AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)])
- ])
-
- # Check for color functions
-
- AC_CACHE_CHECK([for Curses color functions], [ax_cv_plaincurses_color], [
- AC_LINK_IFELSE([AC_LANG_PROGRAM([[
- @%:@define _XOPEN_SOURCE_EXTENDED 1
- @%:@include <curses.h>
- ]], [[
- chtype a = A_BOLD;
- int b = KEY_LEFT;
- chtype c = COLOR_PAIR(1) & A_COLOR;
- initscr();
- init_pair(1, COLOR_WHITE, COLOR_RED);
- ]])],
- [ax_cv_plaincurses_color=yes],
- [ax_cv_plaincurses_color=no])
- ])
- AS_IF([test "x$ax_cv_plaincurses_color" = xyes], [
- ax_cv_curses_color=yes
- AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)])
- ])
-
- # Check for obsolete functions
-
- AC_CACHE_CHECK([for obsolete Curses functions], [ax_cv_plaincurses_obsolete], [
- AC_LINK_IFELSE([AC_LANG_PROGRAM([[
- @%:@include <curses.h>
- ]], [[
- chtype a = A_BOLD;
- int b = KEY_LEFT;
- int g = getattrs(stdscr);
- int h = getcurx(stdscr) + getmaxx(stdscr);
- initscr();
- ]])],
- [ax_cv_plaincurses_obsolete=yes],
- [ax_cv_plaincurses_obsolete=no])
- ])
- AS_IF([test "x$ax_cv_plaincurses_obsolete" = xyes], [
- ax_cv_curses_obsolete=yes
- AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features])
- ])
- ])
-
- AS_IF([test "x$ax_cv_header_curses_h" = xno], [
- AC_MSG_WARN([could not find a working curses.h])
- ])
- ])
- ])
-
- AS_IF([test "x$ax_cv_curses" != xyes], [ax_cv_curses=no])
- AS_IF([test "x$ax_cv_curses_enhanced" != xyes], [ax_cv_curses_enhanced=no])
- AS_IF([test "x$ax_cv_curses_color" != xyes], [ax_cv_curses_color=no])
- AS_IF([test "x$ax_cv_curses_obsolete" != xyes], [ax_cv_curses_obsolete=no])
-
- LIBS=$ax_saved_LIBS
-])dnl
Index: head/biology/samtools/files/ax_with_htslib.m4
===================================================================
--- head/biology/samtools/files/ax_with_htslib.m4
+++ head/biology/samtools/files/ax_with_htslib.m4
@@ -1,140 +0,0 @@
-# ===========================================================================
-# http://www.gnu.org/software/autoconf-archive/ax_with_htslib.html
-# ===========================================================================
-#
-# SYNOPSIS
-#
-# AX_WITH_HTSLIB
-#
-# DESCRIPTION
-#
-# This macro checks whether HTSlib <http://www.htslib.org/> is installed
-# or nearby, and adds a --with-htslib=DIR option to the configure script
-# for specifying the location. It locates either an installation prefix
-# (with 'include' and 'lib' subdirectories) or an HTSlib source tree, as
-# HTSlib is fast-moving and users may wish to use an in-development tree.
-#
-# Different checks occur depending on the --with-htslib argument given:
-#
-# With --with-htslib=DIR, checks whether DIR is a source tree or contains
-# a working installation.
-# By default, searches for a source tree (with a name matching htslib*)
-# within or alongside $srcdir. Produces AC_MSG_ERROR if there are
-# several equally-likely candidates. If there are none, checks for
-# a working default installation.
-# With --with-htslib=system, checks for a working default installation.
-#
-# If a source tree is found or specified, it is added to AC_CONFIG_SUBDIRS
-# (which unfortunately may cause a "you should use literals" warning when
-# autoconf is run).
-#
-# The following output variables are set by this macro:
-#
-# HTSDIR Directory containing HTSlib source tree
-# HTSLIB_CPPFLAGS Preprocessor flags for compiling with HTSlib
-# HTSLIB_LDFLAGS Linker flags for linking with HTSlib
-#
-# The following shell variables may be defined:
-#
-# ax_cv_htslib Set to "yes" if HTSlib was found
-# ax_cv_htslib_which Set to "source", "install", or "none"
-#
-# LICENSE
-#
-# Copyright (C) 2015 Genome Research Ltd
-#
-# Copying and distribution of this file, with or without modification, are
-# permitted in any medium without royalty provided the copyright notice
-# and this notice are preserved. This file is offered as-is, without any
-# warranty.
-
-#serial 1
-
-AC_DEFUN([AX_WITH_HTSLIB],
-[AC_ARG_WITH([htslib],
- [AS_HELP_STRING([--with-htslib=DIR],
- [use the HTSlib source tree or installation in DIR])
-dnl Not indented, to avoid extra whitespace outwith AS_HELP_STRING()
-AS_HELP_STRING([--with-htslib=system],
- [use only a system HTSlib installation])],
- [], [with_htslib=search])
-
-case $with_htslib in
-yes|search)
- AC_MSG_CHECKING([location of HTSlib source tree])
- case $srcdir in
- .) srcp= ;;
- *) srcp=$srcdir/ ;;
- esac
- found=
- for dir in ${srcp}htslib* -- ${srcp}../htslib -- ${srcp}../htslib*
- do
- if test "$dir" = "--"; then
- test -n "$found" && break
- elif test -f "$dir/hts.c" && test -f "$dir/htslib/hts.h"; then
- found="${found}1"
- HTSDIR=$dir
- fi
- done
- if test -z "$found"; then
- AC_MSG_RESULT([none found])
- ax_cv_htslib_which=system
- elif test "$found" = 1; then
- AC_MSG_RESULT([$HTSDIR])
- ax_cv_htslib_which=source
- else
- AC_MSG_RESULT([several directories found])
- AC_MSG_ERROR([use --with-htslib=DIR to select which HTSlib to use])
- fi
- ;;
-no) ax_cv_htslib_which=none ;;
-system) ax_cv_htslib_which=system ;;
-*)
- HTSDIR=$with_htslib
- if test -f "$HTSDIR/hts.c" && test -f "$HTSDIR/htslib/hts.h"; then
- ax_cv_htslib_which=source
- else
- ax_cv_htslib_which=install
- fi
- ;;
-esac
-
-case $ax_cv_htslib_which in
-#source)
-# ax_cv_htslib=yes
-# HTSLIB_CPPFLAGS="-I$HTSDIR"
-# HTSLIB_LDFLAGS="-L$HTSDIR"
-# # We can't use a literal, because $HTSDIR is user-provided and variable
-# AC_CONFIG_SUBDIRS($HTSDIR)
-# ;;
-system)
- AC_CHECK_HEADER([htslib/sam.h],
- [AC_CHECK_LIB(hts, hts_version, [ax_cv_htslib=yes], [ax_cv_htslib=no])],
- [ax_cv_htslib=no], [;])
- ax_cv_htslib_which=install
- HTSDIR=
- HTSLIB_CPPFLAGS=
- HTSLIB_LDFLAGS=
- ;;
-install)
- ax_saved_CPPFLAGS=$CPPFLAGS
- ax_saved_LDFLAGS=$LDFLAGS
- HTSLIB_CPPFLAGS="-I$HTSDIR/include"
- HTSLIB_LDFLAGS="-L$HTSDIR/lib"
- CPPFLAGS="$CPPFLAGS $HTSLIB_CPPFLAGS"
- LDFLAGS="$LDFLAGS $HTSLIB_LDFLAGS"
- AC_CHECK_HEADER([htslib/sam.h],
- [AC_CHECK_LIB(hts, hts_version, [ax_cv_htslib=yes], [ax_cv_htslib=no])],
- [ax_cv_htslib=no], [;])
- HTSDIR=
- CPPFLAGS=$ax_saved_CPPFLAGS
- LDFLAGS=$ax_saved_LDFLAGS
- ;;
-none)
- ax_cv_htslib=no
- ;;
-esac
-
-AC_SUBST([HTSDIR])
-AC_SUBST([HTSLIB_CPPFLAGS])
-AC_SUBST([HTSLIB_LDFLAGS])])
Index: head/biology/samtools/files/patch-Makefile
===================================================================
--- head/biology/samtools/files/patch-Makefile
+++ head/biology/samtools/files/patch-Makefile
@@ -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)
-
-
Index: head/biology/samtools/files/patch-configure.ac
===================================================================
--- head/biology/samtools/files/patch-configure.ac
+++ head/biology/samtools/files/patch-configure.ac
@@ -1,19 +0,0 @@
---- 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],
- [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([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.
-
Index: head/biology/samtools/files/patch-dict.c
===================================================================
--- head/biology/samtools/files/patch-dict.c
+++ head/biology/samtools/files/patch-dict.c
@@ -1,10 +0,0 @@
---- dict.c.orig 2015-12-15 21:26:20 UTC
-+++ dict.c
-@@ -25,6 +25,7 @@ DEALINGS IN THE SOFTWARE. */
- #include <stdio.h>
- #include <zlib.h>
- #include <getopt.h>
-+#include <unistd.h>
- #include "htslib/kseq.h"
- #include "htslib/hts.h"
-
Index: head/biology/samtools/files/patch-errmod.c
===================================================================
--- head/biology/samtools/files/patch-errmod.c
+++ head/biology/samtools/files/patch-errmod.c
@@ -1,16 +0,0 @@
---- errmod.c.orig 2015-12-15 21:26:20 UTC
-+++ errmod.c
-@@ -24,6 +24,13 @@ FROM, OUT OF OR IN CONNECTION WITH THE S
- DEALINGS IN THE SOFTWARE. */
-
- #include <math.h>
-+
-+#include <sys/param.h>
-+#if defined(__FreeBSD__) && (__FreeBSD_version < 1000034)
-+# define logl(x) log(x)
-+# define expl(x) exp(x)
-+#endif
-+
- #include "errmod.h"
- #include "htslib/ksort.h"
- KSORT_INIT_GENERIC(uint16_t)
Index: head/biology/samtools/files/patch-test_test.pl
===================================================================
--- head/biology/samtools/files/patch-test_test.pl
+++ head/biology/samtools/files/patch-test_test.pl
@@ -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}");
Index: head/biology/samtools/files/pkg-message.in
===================================================================
--- head/biology/samtools/files/pkg-message.in
+++ head/biology/samtools/files/pkg-message.in
@@ -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.

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