biology/bcftools: Upgrade to 1.10.2

Numerous bug fixes and enhancements since 1.9:
https://github.com/samtools/bcftools/tags

Take maintainership per ports/248089.

PR:             ports/248089

6 files changed, 69 insertions, 78 deletions

diff --git a/biology/bcftools/Makefile b/biology/bcftools/Makefile
index 73e4a9fef542..8e45ca34e041 100644
--- a/biology/bcftools/Makefile
+++ b/biology/bcftools/Makefile
@@ -2,33 +2,30 @@
 # $FreeBSD$
 
 PORTNAME=	bcftools
-PORTVERSION=	1.9
-PORTREVISION=	2
+PORTVERSION=	1.10.2
 CATEGORIES=	biology
 
-MAINTAINER=	cartwright@asu.edu
+MAINTAINER=	jwb@FreeBSD.org
 COMMENT=	Tools for manipulating next-generation sequencing data
 
 LICENSE=	MIT
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
-BUILD_DEPENDS=	htslib>=1.6:biology/htslib
-LIB_DEPENDS=	libhts.so:biology/htslib
+LIB_DEPENDS=	libhts.so.3:biology/htslib
 TEST_DEPENDS=	bash:shells/bash
 
-USES=		autoreconf gmake localbase \
-		perl5 python:env shebangfix
+USES=		autoreconf gmake localbase perl5 python:env shebangfix
 
 USE_GITHUB=	yes
-GH_ACCOUNT=	samtools
-
 USE_LDCONFIG=	${PREFIX}/libexec/${PORTNAME}
 USE_PERL5=	test
+
+GH_ACCOUNT=	samtools
 GNU_CONFIGURE=	yes
 SHEBANG_FILES=	misc/* test/test.pl
 
-OPTIONS_DEFINE=	GPL
-GPL_DESC=	Enable modules that rely on GPL code
+OPTIONS_DEFINE=		GPL
+GPL_DESC=		Enable modules that rely on GPL code
 OPTIONS_DEFAULT=	GPL
 
 GPL_LIB_DEPENDS=	libgsl.so:math/gsl
@@ -43,22 +40,22 @@ LICENSE_COMB=	multi
 
 TEST_TARGET=	test
 
-post-patch:
-	@${REINPLACE_CMD} -e 's|@PORTVERSION@|${PORTVERSION}|g' ${WRKSRC}/configure.ac
+pre-configure:
+	@${REINPLACE_CMD} -e 's|@PORTVERSION@|${PORTVERSION}|g' \
+		${WRKSRC}/configure.ac
 
 post-install:
-	${MV} ${STAGEDIR}${PREFIX}/bin/samtools_misc/color-chrs.pl \
+	${MV} ${STAGEDIR}${PREFIX}/bin/color-chrs.pl \
 		${STAGEDIR}${PREFIX}/bin/color-chrs
-	${MV} ${STAGEDIR}${PREFIX}/bin/samtools_misc/guess-ploidy.py\
+	${MV} ${STAGEDIR}${PREFIX}/bin/guess-ploidy.py\
 	       ${STAGEDIR}${PREFIX}/bin/guess-ploidy
-	${MV} /${STAGEDIR}${PREFIX}/bin/samtools_misc/plot-roh.py \
+	${MV} /${STAGEDIR}${PREFIX}/bin/plot-roh.py \
 		${STAGEDIR}${PREFIX}/bin/plot-roh
-	${MV} ${STAGEDIR}${PREFIX}/bin/samtools_misc/run-roh.pl \
+	${MV} ${STAGEDIR}${PREFIX}/bin/run-roh.pl \
 		${STAGEDIR}${PREFIX}/bin/run-roh
-	${MV} ${STAGEDIR}${PREFIX}/bin/samtools_misc/vcfutils.pl \
+	${MV} ${STAGEDIR}${PREFIX}/bin/vcfutils.pl \
 		${STAGEDIR}${PREFIX}/bin/vcfutils
-	${MV} ${STAGEDIR}${PREFIX}/bin/samtools_misc/plot-vcfstats \
+	${MV} ${STAGEDIR}${PREFIX}/bin/plot-vcfstats \
 		${STAGEDIR}${PREFIX}/bin/
-	${RMDIR} ${STAGEDIR}${PREFIX}/bin/samtools_misc/
 
 .include <bsd.port.mk>
diff --git a/biology/bcftools/distinfo b/biology/bcftools/distinfo
index 92f009bcffd3..9e0401b10cfd 100644
--- a/biology/bcftools/distinfo
+++ b/biology/bcftools/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1532903716
-SHA256 (samtools-bcftools-1.9_GH0.tar.gz) = 223b90c9a9b11576174384de70abe8e8394aef1b45c7324e4bf875d0f344e96e
-SIZE (samtools-bcftools-1.9_GH0.tar.gz) = 2394968
+TIMESTAMP = 1595166811
+SHA256 (samtools-bcftools-1.10.2_GH0.tar.gz) = 13277c17047152951e0bfe4467adc7768571b18e26610d206cab5560de5a395a
+SIZE (samtools-bcftools-1.10.2_GH0.tar.gz) = 2880994
diff --git a/biology/bcftools/files/patch-Makefile b/biology/bcftools/files/patch-Makefile
index 6e9f772d2b8b..b44cd69acd3e 100644
--- a/biology/bcftools/files/patch-Makefile
+++ b/biology/bcftools/files/patch-Makefile
@@ -1,40 +1,40 @@
---- Makefile.orig	2018-07-18 08:34:29 UTC
+--- Makefile.orig	2019-12-19 09:57:32 UTC
 +++ Makefile
-@@ -22,10 +22,10 @@
+@@ -22,13 +22,12 @@
  # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
  # DEALINGS IN THE SOFTWARE.
  
 -CC       = gcc
+-AR       = ar
+-RANLIB   = ranlib
 -CPPFLAGS =
--CFLAGS   = -g -Wall -Wc++-compat -O2
+-CFLAGS   = -g -Wall -O2
 -LDFLAGS  =
-+CC       ?= cc
-+CPPFLAGS +=
-+CFLAGS   += -Wall
-+LDFLAGS  +=
- LIBS     =
+-LIBS     =
++CC       ?= gcc
++AR       ?= ar
++RANLIB   ?= ranlib
++CPPFLAGS ?=
++CFLAGS   ?= -g -Wall -O2
++LDFLAGS  ?=
  
  DYNAMIC_FLAGS = -rdynamic
-@@ -42,26 +42,25 @@ OBJS     = main.o vcfindex.o tabix.o \
-            vcfsort.o \
+ PLUGINS_ENABLED = yes
+@@ -45,7 +44,8 @@ OBJS     = main.o vcfindex.o tabix.o \
             ccall.o em.o prob1.o kmin.o # the original samtools calling
+ PLUGIN_OBJS = vcfplugin.o
  
 -prefix      = /usr/local
-+prefix      = ${PREFIX}
++PREFIX      ?= /usr/local
++prefix      = $(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
- # Installation location for $(PLUGINS)
- plugindir   = $(libexecdir)/bcftools
- pluginpath  = $(plugindir)
+@@ -58,13 +58,13 @@ pluginpath  = $(plugindir)
  # Installation location for $(MISC_PROGRAMS) and $(MISC_SCRIPTS)
--misc_bindir = $(bindir)
-+misc_bindir = $(bindir)/samtools_misc
+ misc_bindir = $(bindir)
  
++# Use BSD_INSTALL_PROGRAM to strip when WITH_DEBUG not set
  MKDIR_P = mkdir -p
 -INSTALL = install -p
 -INSTALL_DATA    = $(INSTALL) -m 644
@@ -50,25 +50,16 @@
  
  PROGRAMS = bcftools
  MISC_SCRIPTS = \
-@@ -77,7 +76,7 @@ all: $(PROGRAMS) $(TEST_PROGRAMS) plugin
- 
- ALL_CPPFLAGS = -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS)
- ALL_LDFLAGS  = $(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.
-@@ -131,7 +130,7 @@ print-version:
+@@ -141,7 +141,7 @@ print-version:
  ifdef USE_GPL
      main.o : EXTRA_CPPFLAGS += -DUSE_GPL
      OBJS += polysomy.o peakfit.o
 -    GSL_LIBS ?= -lgsl -lcblas
-+    GSL_LIBS ?= -lgsl -lgslcblas
++    GSL_LIBS ?= -lgslcblas
  endif
  
- bcftools: $(OBJS) $(HTSLIB)
-@@ -278,7 +277,7 @@ docs: doc/bcftools.1 doc/bcftools.html
+ print-%:
+@@ -320,7 +320,7 @@ 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: $(PROGRAMS) $(PLUGINS)
diff --git a/biology/bcftools/files/patch-prob1.c b/biology/bcftools/files/patch-prob1.c
deleted file mode 100644
index 9fdaa65b4f5a..000000000000
--- a/biology/bcftools/files/patch-prob1.c
+++ /dev/null
@@ -1,15 +0,0 @@
---- prob1.c.orig	2017-09-28 11:22:48 UTC
-+++ prob1.c
-@@ -33,6 +33,12 @@ THE SOFTWARE.  */
- #include <zlib.h>
- #include "prob1.h"
- 
-+#include <sys/param.h>
-+#if defined(__FreeBSD__) && (__FreeBSD_version < 1000034)
-+#	define logl(x) log(x)
-+#	define expl(x) exp(x)
-+#endif
-+
- // #include "kstring.h"
- // #include "kseq.h"
- // KSTREAM_INIT(gzFile, gzread, 16384)
diff --git a/biology/bcftools/files/patch-test_test.pl b/biology/bcftools/files/patch-test_test.pl
index a42f062d3106..079f0e7fe78b 100644
--- a/biology/bcftools/files/patch-test_test.pl
+++ b/biology/bcftools/files/patch-test_test.pl
@@ -1,29 +1,38 @@
---- test/test.pl.orig	2017-10-18 09:33:24 UTC
+--- test/test.pl.orig	2020-07-21 20:49:56 UTC
 +++ test/test.pl
-@@ -381,7 +381,7 @@ sub _cmd
+@@ -610,7 +610,7 @@ 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]: $!");
++        exec('bash', '-o','pipefail','-c', $cmd) or error("Cannot execute the command [/usr/local/bin/sh -o pipefail -c $cmd]: $!");
      }
      return ($? >> 8, join('',@out));
  }
-@@ -782,7 +782,7 @@ sub test_usage
+@@ -622,7 +622,7 @@ sub _cmd3
+     my $pid = fork();
+     if ( !$pid )
+     {
+-        exec('/bin/bash', '-o','pipefail','-c', "($cmd) 2>$tmp.e >$tmp.o");
++        exec('bash', '-o','pipefail','-c', "($cmd) 2>$tmp.e >$tmp.o");
+     }
+     waitpid($pid,0);
+ 
+@@ -1063,7 +1063,7 @@ 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; }
++    if ( $out =~ m/bash.*no.*such/i ) { failed($opts,$test,"could not run $commandpath: $out"); return; }
  
      my @sections = ($out =~ m/(^[A-Za-z]+.*?)(?:(?=^[A-Za-z]+:)|\z)/msg);
  
-@@ -833,7 +833,7 @@ sub test_usage_subcommand
+@@ -1118,7 +1118,7 @@ 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; }
++    if ( $out =~ m/bash.*no.*such/i ) { failed($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/pkg-plist b/biology/bcftools/pkg-plist
index 5b68f6191cfb..cc32e1b8aa50 100644
--- a/biology/bcftools/pkg-plist
+++ b/biology/bcftools/pkg-plist
@@ -8,7 +8,9 @@ bin/vcfutils
 libexec/bcftools/GTisec.so
 libexec/bcftools/GTsubset.so
 libexec/bcftools/ad-bias.so
+libexec/bcftools/add-variantkey.so
 libexec/bcftools/af-dist.so
+libexec/bcftools/allele-length.so
 libexec/bcftools/check-ploidy.so
 libexec/bcftools/check-sparsity.so
 libexec/bcftools/color-chrs.so
@@ -22,15 +24,22 @@ libexec/bcftools/fixploidy.so
 libexec/bcftools/fixref.so
 libexec/bcftools/frameshifts.so
 libexec/bcftools/guess-ploidy.so
+libexec/bcftools/gvcfz.so
 libexec/bcftools/impute-info.so
+libexec/bcftools/indel-stats.so
 libexec/bcftools/isecGT.so
 libexec/bcftools/mendelian.so
 libexec/bcftools/missing2ref.so
+libexec/bcftools/parental-origin.so
 libexec/bcftools/prune.so
+libexec/bcftools/remove-overlaps.so
 libexec/bcftools/setGT.so
 libexec/bcftools/smpl-stats.so
+libexec/bcftools/split-vep.so
 libexec/bcftools/split.so
 libexec/bcftools/tag2tag.so
+libexec/bcftools/trio-dnm.so
 libexec/bcftools/trio-stats.so
 libexec/bcftools/trio-switch-rate.so
+libexec/bcftools/variantkey-hex.so
 man/man1/bcftools.1.gz