biology/bcf-score: Update to 1.20

Numerous bug fixes and enhancements since 1.16

Reported by:    portscout

7 files changed, 42 insertions, 56 deletions

diff --git a/biology/bcf-score/Makefile b/biology/bcf-score/Makefile
index f183641f4a4f..d29f1e583120 100644
--- a/biology/bcf-score/Makefile
+++ b/biology/bcf-score/Makefile
@@ -1,9 +1,9 @@
 PORTNAME=	bcf-score
-DISTVERSION=	1.16
-PORTREVISION=	1
+DISTVERSION=	1.20
 CATEGORIES=	biology
 MASTER_SITES=	https://software.broadinstitute.org/software/score/
-DISTFILES+=	score_${DISTVERSION}-20221221.tar.gz
+# Get this right, or ports will download bcftools in it's place via tuple
+DISTFILES+=	score_${DISTVERSION}-20240505.tar.gz
 
 MAINTAINER=	jwb@FreeBSD.org
 COMMENT=	Bcftools plugins for GWAS-VCF summary statistics files
@@ -11,9 +11,10 @@ WWW=		https://software.broadinstitute.org/software/score/
 
 LICENSE=	MIT
 
-LIB_DEPENDS=	libhts.so:biology/htslib
-BUILD_DEPENDS=	bash:shells/bash
-RUN_DEPENDS=	bcftools>=${PORTVERSION}:biology/bcftools
+BUILD_DEPENDS=	htslib>=1.21:biology/htslib
+LIB_DEPENDS=	libhts.so:biology/htslib libcholmod.so:math/suitesparse-cholmod
+TEST_DEPENDS=	bash:shells/bash
+RUN_DEPENDS=	bash:shells/bash bcftools>=${PORTVERSION}:biology/bcftools
 
 USES=		autoreconf gmake localbase perl5 python:env shebangfix
 USE_GITHUB=	yes
@@ -21,23 +22,27 @@ USE_PERL5=	test
 
 GH_ACCOUNT=	samtools
 GH_PROJECT=	bcftools
-GH_TAGNAME=	1.17
+GH_TAGNAME=	1.21
 GNU_CONFIGURE=	yes
 SHEBANG_FILES=	misc/* test/test.pl
 
-post-extract:
-	@${CP} ${WRKDIR}/*.c ${WRKDIR}/*.h ${WRKSRC}/plugins
-	@${MKDIR} ${WRKSRC}/bcf-score
-	@${CP} ${WRKDIR}/*.R ${WRKSRC}/bcf-score
+# From pgs.mk
+CFLAGS+=	-isystem ${LOCALBASE}/include/suitesparse
+LDFLAGS+=	-lcholmod
 
 pre-configure:
 	@${REINPLACE_CMD} -e 's|@PORTVERSION@|${PORTVERSION}|g' \
 		${WRKSRC}/configure.ac
 
+post-extract:
+	@${CP} ${WRKDIR}/*.c ${WRKDIR}/*.h ${WRKSRC}/plugins
+	@${MKDIR} ${WRKSRC}/bcf-score
+	@${CP} ${WRKDIR}/*.R ${WRKSRC}/bcf-score
+
 # One .so for each .c in the score distfile
 do-install:
 	${MKDIR} ${STAGEDIR}${PREFIX}/libexec/bcftools
-	${INSTALL_PROGRAM} ${WRKSRC}/plugins/blupx.so \
+	${INSTALL_PROGRAM} ${WRKSRC}/plugins/blup.so \
 		${STAGEDIR}${PREFIX}/libexec/bcftools
 	${INSTALL_PROGRAM} ${WRKSRC}/plugins/liftover.so \
 		${STAGEDIR}${PREFIX}/libexec/bcftools
@@ -45,6 +50,8 @@ do-install:
 		${STAGEDIR}${PREFIX}/libexec/bcftools
 	${INSTALL_PROGRAM} ${WRKSRC}/plugins/munge.so \
 		${STAGEDIR}${PREFIX}/libexec/bcftools
+	${INSTALL_PROGRAM} ${WRKSRC}/plugins/pgs.so \
+		${STAGEDIR}${PREFIX}/libexec/bcftools
 	${INSTALL_PROGRAM} ${WRKSRC}/plugins/score.so \
 		${STAGEDIR}${PREFIX}/libexec/bcftools
 	(cd ${WRKSRC}/bcf-score && ${COPYTREE_SHARE} . ${STAGEDIR}${DATADIR})
diff --git a/biology/bcf-score/distinfo b/biology/bcf-score/distinfo
index d343300fb841..fb0644c4567b 100644
--- a/biology/bcf-score/distinfo
+++ b/biology/bcf-score/distinfo
@@ -1,5 +1,5 @@
-TIMESTAMP = 1677335027
-SHA256 (score_1.16-20221221.tar.gz) = f5f7331f2f670ea26cbc48a924e1467ac13c69aaf3b2a56599e3decda9375c0b
-SIZE (score_1.16-20221221.tar.gz) = 61927
-SHA256 (samtools-bcftools-1.16-1.17_GH0.tar.gz) = e6fdb4c94b531671ea8a0b00cb9245aa2602f6c4480621e45dac76338f590b9e
-SIZE (samtools-bcftools-1.16-1.17_GH0.tar.gz) = 3481344
+TIMESTAMP = 1727475307
+SHA256 (score_1.20-20240505.tar.gz) = c2ac510f0a48e3d2e61d1a9e219e030b1268cdcf3bf987217bbd16740d962d41
+SIZE (score_1.20-20240505.tar.gz) = 96852
+SHA256 (samtools-bcftools-1.20-1.21_GH0.tar.gz) = 7484695c5d833fb1a89c2b886ec302db0514ba3c8e5ef7397b9302fa8bd37f8d
+SIZE (samtools-bcftools-1.20-1.21_GH0.tar.gz) = 3665160
diff --git a/biology/bcf-score/files/patch-Makefile b/biology/bcf-score/files/patch-Makefile
index 3299954ae45b..55d6f64d426d 100644
--- a/biology/bcf-score/files/patch-Makefile
+++ b/biology/bcf-score/files/patch-Makefile
@@ -1,6 +1,6 @@
---- Makefile.orig	2021-03-17 09:16:18 UTC
+--- Makefile.orig	2024-09-12 15:06:36 UTC
 +++ Makefile
-@@ -58,13 +58,14 @@ pluginpath  = $(plugindir)
+@@ -59,13 +59,14 @@ misc_bindir = $(bindir)
  # Installation location for $(MISC_PROGRAMS) and $(MISC_SCRIPTS)
  misc_bindir = $(bindir)
  
@@ -12,22 +12,22 @@
 -INSTALL_PROGRAM = $(INSTALL)
 -INSTALL_SCRIPT  = $(INSTALL_PROGRAM)
 +# Use BSD_INSTALL_PROGRAM to strip when WITH_DEBUG not set
-+MKDIR_P 	= mkdir -p
-+INSTALL 	= install -p
-+INSTALL_DATA    = ${BSD_INSTALL_DATA}
-+INSTALL_DIR     = $(MKDIR_P)
-+INSTALL_MAN     = ${BSD_INSTALL_MAN}
-+INSTALL_PROGRAM = ${BSD_INSTALL_PROGRAM}
-+INSTALL_SCRIPT  = ${BSD_INSTALL_SCRIPT}
++MKDIR_P		= mkdir -p
++INSTALL		= install -p
++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 = bcftools
  MISC_SCRIPTS = \
-@@ -142,7 +143,7 @@ print-version:
- ifdef USE_GPL
+@@ -144,7 +145,7 @@ ifdef USE_GPL
      main.o : EXTRA_CPPFLAGS += -DUSE_GPL
      OBJS += polysomy.o peakfit.o
--    GSL_LIBS ?= -lgsl -lcblas
-+    GSL_LIBS ?= -lgslcblas
+     ifndef GSL_LIBS
+-        GSL_LIBS += -lgsl -lcblas
++        GSL_LIBS += -lgslcblas
+     endif
  endif
  
- print-%:
diff --git a/biology/bcf-score/files/patch-configure.ac b/biology/bcf-score/files/patch-configure.ac
index ca845d2ad85f..31087a94e97f 100644
--- a/biology/bcf-score/files/patch-configure.ac
+++ b/biology/bcf-score/files/patch-configure.ac
@@ -1,6 +1,6 @@
---- configure.ac.orig	2018-07-18 08:34:29 UTC
+--- configure.ac.orig	2024-09-27 11:57:52 UTC
 +++ configure.ac
-@@ -23,7 +23,7 @@
+@@ -23,7 +23,7 @@ dnl Process this file with autoconf to produce a confi
  # DEALINGS IN THE SOFTWARE.
  
  dnl Process this file with autoconf to produce a configure script
diff --git a/biology/bcf-score/files/patch-plugins_munge.c b/biology/bcf-score/files/patch-plugins_munge.c
deleted file mode 100644
index 8906f57a0a73..000000000000
--- a/biology/bcf-score/files/patch-plugins_munge.c
+++ /dev/null
@@ -1,11 +0,0 @@
---- plugins/munge.c.orig	2023-07-16 07:57:54 UTC
-+++ plugins/munge.c
-@@ -120,7 +120,7 @@ int tsv_read_string(tsv_t *tsv, bcf1_t *rec, void *usr
-     return 0;
- }
- 
--static const int (*tsv_setters[])(tsv_t *tsv, bcf1_t *rec, void *usr) = {tsv_setter_id_flexible,         // SNP
-+static int (*tsv_setters[])(tsv_t *tsv, bcf1_t *rec, void *usr) = {tsv_setter_id_flexible,         // SNP
-                                                                          tsv_setter_pos_flexible,        // BP
-                                                                          tsv_setter_chrom_flexible,      // CHR
-                                                                          tsv_read_allele,                // A1
diff --git a/biology/bcf-score/files/patch-plugins_score.c b/biology/bcf-score/files/patch-plugins_score.c
deleted file mode 100644
index c90a66f313b6..000000000000
--- a/biology/bcf-score/files/patch-plugins_score.c
+++ /dev/null
@@ -1,11 +0,0 @@
---- plugins/score.c.orig	2023-07-16 08:04:54 UTC
-+++ plugins/score.c
-@@ -140,7 +140,7 @@ static int tsv_read_allele(tsv_t *tsv, bcf1_t *rec, vo
-     return 0;
- }
- 
--static const int (*tsv_setters[])(tsv_t *tsv, bcf1_t *rec, void *usr) = {tsv_setter_id_flexible,         // SNP
-+static int (*tsv_setters[])(tsv_t *tsv, bcf1_t *rec, void *usr) = {tsv_setter_id_flexible,         // SNP
-                                                                          tsv_setter_pos_flexible,        // BP
-                                                                          tsv_setter_chrom_flexible,      // CHR
-                                                                          tsv_read_allele,                // A1
diff --git a/biology/bcf-score/pkg-plist b/biology/bcf-score/pkg-plist
index 719a907bf251..f9741a4d9fdf 100644
--- a/biology/bcf-score/pkg-plist
+++ b/biology/bcf-score/pkg-plist
@@ -1,6 +1,7 @@
-libexec/bcftools/blupx.so
+libexec/bcftools/blup.so
 libexec/bcftools/liftover.so
 libexec/bcftools/metal.so
 libexec/bcftools/munge.so
+libexec/bcftools/pgs.so
 libexec/bcftools/score.so
 %%DATADIR%%/assoc_plot.R