biology/biolibc: Update to 0.1.3

Import sam_buff_t class and VCF functions from ad2vcf
Add BED and GFF support
Isolate headers under include/biolibc
Numerous small enhancements and fixes

Upstream change log: https://github.com/auerlab/biolibc/releases

4 files changed, 52 insertions, 16 deletions

diff --git a/biology/biolibc/Makefile b/biology/biolibc/Makefile
index 1753661d6e6..2358fc0705d 100644
--- a/biology/biolibc/Makefile
+++ b/biology/biolibc/Makefile
@@ -1,6 +1,6 @@
-# $NetBSD: Makefile,v 1.1 2021/03/24 15:20:08 bacon Exp $
+# $NetBSD: Makefile,v 1.2 2021/06/11 17:04:55 bacon Exp $
 
-DISTNAME=	biolibc-0.1.1
+DISTNAME=	biolibc-0.1.3
 CATEGORIES=	biology
 MASTER_SITES=	${MASTER_SITE_GITHUB:=auerlab/}
 
@@ -9,4 +9,19 @@ HOMEPAGE=	https://github.com/auerlab/biolibc
 COMMENT=	Low-level high-performance bioinformatics library
 LICENSE=	2-clause-bsd
 
+.include "../../mk/bsd.prefs.mk"
+
+.if ${OPSYS} == Darwin
+BUILD_TARGET=	apple
+INSTALL_TARGET=	apple-install
+.else
+INSTALL_TARGET=	install-strip
+.endif
+
+MAKE_ENV+=	DYLIB_PATH=${PREFIX}/lib
+
+pre-build:
+	cd ${WRKSRC} && ${MAKE} PREFIX=${PREFIX} depend
+
+.include "../../devel/libxtend/buildlink3.mk"
 .include "../../mk/bsd.pkg.mk"
diff --git a/biology/biolibc/PLIST b/biology/biolibc/PLIST
index f38ee7d7b30..e669968eba2 100644
--- a/biology/biolibc/PLIST
+++ b/biology/biolibc/PLIST
@@ -1,7 +1,29 @@
-@comment $NetBSD: PLIST,v 1.1 2021/03/24 15:20:08 bacon Exp $
-include/biostring.h
-include/dsvio.h
-include/samio.h
-include/vcfio.h
+@comment $NetBSD: PLIST,v 1.2 2021/06/11 17:04:55 bacon Exp $
+include/biolibc/bed.h
+include/biolibc/biolibc.h
+include/biolibc/dsv.h
+include/biolibc/gff.h
+include/biolibc/plist.h
+include/biolibc/sam-buff.h
+include/biolibc/sam.h
+include/biolibc/vcf.h
 lib/libbiolibc.a
-man/man1/biolibc.1
+lib/libbiolibc.so
+lib/libbiolibc.so.2
+lib/libbiolibc.so.2.0
+man/man3/bed_check_order.3
+man/man3/bed_gff_cmp.3
+man/man3/bed_read_feature.3
+man/man3/bed_set_chromosome.3
+man/man3/bed_set_end_pos.3
+man/man3/bed_set_fields.3
+man/man3/bed_set_name.3
+man/man3/bed_set_rgb_str.3
+man/man3/bed_set_score.3
+man/man3/bed_set_start_pos.3
+man/man3/bed_set_strand.3
+man/man3/bed_set_thick_end_pos.3
+man/man3/bed_set_thick_start_pos.3
+man/man3/bed_skip_header.3
+man/man3/bed_write_feature.3
+man/man3/biolibc.3
diff --git a/biology/biolibc/buildlink3.mk b/biology/biolibc/buildlink3.mk
index 8e9ad1527c7..ffee918c1d8 100644
--- a/biology/biolibc/buildlink3.mk
+++ b/biology/biolibc/buildlink3.mk
@@ -1,13 +1,12 @@
-# $NetBSD: buildlink3.mk,v 1.1 2021/03/24 15:20:08 bacon Exp $
+# $NetBSD: buildlink3.mk,v 1.2 2021/06/11 17:04:55 bacon Exp $
 
 BUILDLINK_TREE+=	biolibc
 
 .if !defined(BIOLIBC_BUILDLINK3_MK)
 BIOLIBC_BUILDLINK3_MK:=
 
-BUILDLINK_API_DEPENDS.biolibc+=	biolibc>=0.1.1
+BUILDLINK_API_DEPENDS.biolibc+=	biolibc>=0.1.3
 BUILDLINK_PKGSRCDIR.biolibc?=	../../biology/biolibc
-BUILDLINK_DEPMETHOD.biolibc?=	build
 .endif	# BIOLIBC_BUILDLINK3_MK
 
 BUILDLINK_TREE+=	-biolibc
diff --git a/biology/biolibc/distinfo b/biology/biolibc/distinfo
index 6ccf45d675d..16c58e996c8 100644
--- a/biology/biolibc/distinfo
+++ b/biology/biolibc/distinfo
@@ -1,6 +1,6 @@
-$NetBSD: distinfo,v 1.1 2021/03/24 15:20:08 bacon Exp $
+$NetBSD: distinfo,v 1.2 2021/06/11 17:04:55 bacon Exp $
 
-SHA1 (biolibc-0.1.1.tar.gz) = 7c5861ebfd97dd6d92a489297244debe3c48af05
-RMD160 (biolibc-0.1.1.tar.gz) = 95b9fce0efe0c68be43bea5f875a72efce98f58e
-SHA512 (biolibc-0.1.1.tar.gz) = 673fa88ab48bbbcd5d3256a244472fdaa2c76fc5c0fa78663179487f8d8e9c65aaff593220859a54ed6e17f76a080cabe7e5866d12ab3948996e28b0d05d12bc
-Size (biolibc-0.1.1.tar.gz) = 11770 bytes
+SHA1 (biolibc-0.1.3.tar.gz) = e3381720674b2bc27ec4bfa9c0823fa2012d3422
+RMD160 (biolibc-0.1.3.tar.gz) = e857f91609d71ad6698534d5cf47c070c5538c94
+SHA512 (biolibc-0.1.3.tar.gz) = 92c08cfec13e99c33d2a275ce5dc69c0bd4160a2d7851c2693b3c825a95a0b6797adfd7ca606d70511b63c8e275ab635f88af8ad639556ebe318b1086b59ac3e
+Size (biolibc-0.1.3.tar.gz) = 30046 bytes