From 09c70c7488989b1a37f4da6a447871c5bea06ee0 Mon Sep 17 00:00:00 2001
From: "Jason W. Bacon" <jwb@FreeBSD.org>
Date: Thu, 5 Jan 2023 17:21:03 -0600
Subject: [PATCH] biology/bio-mocha: Update to 1.16

New release to sync with bcftools

Changes: https://github.com/freeseek/mocha/commits/master
---
 biology/bio-mocha/Makefile  | 10 ++++------
 biology/bio-mocha/distinfo  | 10 +++++-----
 biology/bio-mocha/pkg-plist |  2 --
 3 files changed, 9 insertions(+), 13 deletions(-)

diff --git a/biology/bio-mocha/Makefile b/biology/bio-mocha/Makefile
index fb552c0676e7a..33147346e72dd 100644
--- a/biology/bio-mocha/Makefile
+++ b/biology/bio-mocha/Makefile
@@ -1,9 +1,8 @@
 PORTNAME=	bio-mocha
-DISTVERSION=	1.14
-PORTREVISION=	1
+DISTVERSION=	1.16
 CATEGORIES=	biology
 MASTER_SITES=	https://software.broadinstitute.org/software/mocha/
-DISTFILES+=	${PORTNAME}_${DISTVERSION}-20220112.tar.gz
+DISTFILES+=	${PORTNAME}_${DISTVERSION}-20221221.tar.gz
 
 MAINTAINER=	jwb@FreeBSD.org
 COMMENT=	Bcftools plugin for mosaic chromosomal alteration analysis
@@ -21,7 +20,7 @@ USE_PERL5=	test
 
 GH_ACCOUNT=	samtools
 GH_PROJECT=	bcftools
-GH_TAGNAME=	1.15
+GH_TAGNAME=	1.16
 GNU_CONFIGURE=	yes
 SHEBANG_FILES=	misc/* test/test.pl
 
@@ -34,6 +33,7 @@ pre-configure:
 	@${REINPLACE_CMD} -e 's|@PORTVERSION@|${PORTVERSION}|g' \
 		${WRKSRC}/configure.ac
 
+# One .so for each .c in the mocha distfile
 do-install:
 	${MKDIR} ${STAGEDIR}${PREFIX}/libexec/bcftools
 	${INSTALL_PROGRAM} ${WRKSRC}/plugins/extendFMT.so \
@@ -42,8 +42,6 @@ do-install:
 		${STAGEDIR}${PREFIX}/libexec/bcftools
 	${INSTALL_PROGRAM} ${WRKSRC}/plugins/mochatools.so \
 		${STAGEDIR}${PREFIX}/libexec/bcftools
-	${INSTALL_PROGRAM} ${WRKSRC}/plugins/score.so \
-		${STAGEDIR}${PREFIX}/libexec/bcftools
 	${INSTALL_PROGRAM} ${WRKSRC}/plugins/trio-phase.so \
 		${STAGEDIR}${PREFIX}/libexec/bcftools
 	(cd ${WRKSRC}/MoCha && ${COPYTREE_SHARE} . ${STAGEDIR}${DATADIR})
diff --git a/biology/bio-mocha/distinfo b/biology/bio-mocha/distinfo
index 6f18a06e9fb52..c5a05127a3d6b 100644
--- a/biology/bio-mocha/distinfo
+++ b/biology/bio-mocha/distinfo
@@ -1,5 +1,5 @@
-TIMESTAMP = 1645832006
-SHA256 (bio-mocha_1.14-20220112.tar.gz) = 189a522418f12cbb04e6c5ccae130dbae1682907808f4cb594af4ff386651068
-SIZE (bio-mocha_1.14-20220112.tar.gz) = 75910
-SHA256 (samtools-bcftools-1.14-1.15_GH0.tar.gz) = 6b263270c62b156d2604150ca7e64b06a80282e049759b2668de24cbce1b1946
-SIZE (samtools-bcftools-1.14-1.15_GH0.tar.gz) = 3347901
+TIMESTAMP = 1672095342
+SHA256 (bio-mocha_1.16-20221221.tar.gz) = 576cbdda53760f353fc8fd989751716b1d4f8c5e1921f838c263476282cced86
+SIZE (bio-mocha_1.16-20221221.tar.gz) = 68625
+SHA256 (samtools-bcftools-1.16_GH0.tar.gz) = c44c85a04e058e1f1eceeb712106031100bbd700b8ff3f623f7ff872469a4ba3
+SIZE (samtools-bcftools-1.16_GH0.tar.gz) = 3432435
diff --git a/biology/bio-mocha/pkg-plist b/biology/bio-mocha/pkg-plist
index 4604936e8e0f3..a56018707fc6e 100644
--- a/biology/bio-mocha/pkg-plist
+++ b/biology/bio-mocha/pkg-plist
@@ -1,9 +1,7 @@
 libexec/bcftools/extendFMT.so
 libexec/bcftools/mocha.so
 libexec/bcftools/mochatools.so
-libexec/bcftools/score.so
 libexec/bcftools/trio-phase.so
-%%DATADIR%%/assoc_plot.R
 %%DATADIR%%/mocha_plot.R
 %%DATADIR%%/pileup_plot.R
 %%DATADIR%%/summary_plot.R