head 1.14; access; symbols pkgsrc-2023Q4:1.14.0.2 pkgsrc-2023Q4-base:1.14 pkgsrc-2023Q3:1.13.0.2 pkgsrc-2023Q3-base:1.13 pkgsrc-2023Q2:1.12.0.2 pkgsrc-2023Q2-base:1.12 pkgsrc-2023Q1:1.11.0.2 pkgsrc-2023Q1-base:1.11 pkgsrc-2022Q4:1.10.0.2 pkgsrc-2022Q4-base:1.10 pkgsrc-2022Q3:1.9.0.4 pkgsrc-2022Q3-base:1.9 pkgsrc-2022Q2:1.9.0.2 pkgsrc-2022Q2-base:1.9 pkgsrc-2022Q1:1.8.0.2 pkgsrc-2022Q1-base:1.8 pkgsrc-2021Q4:1.7.0.2 pkgsrc-2021Q4-base:1.7 pkgsrc-2021Q3:1.6.0.2 pkgsrc-2021Q3-base:1.6 pkgsrc-2021Q2:1.3.0.2 pkgsrc-2021Q2-base:1.3 pkgsrc-2021Q1:1.1.0.2 pkgsrc-2021Q1-base:1.1; locks; strict; comment @# @; 1.14 date 2023.10.28.20.31.40; author bacon; state Exp; branches; next 1.13; commitid FD7CduPkfxmVVqKE; 1.13 date 2023.08.12.14.49.18; author bacon; state Exp; branches; next 1.12; commitid Rv92KGtcXouGvvAE; 1.12 date 2023.06.14.18.41.24; author bacon; state Exp; branches; next 1.11; commitid M0EBbRZdppaeHWsE; 1.11 date 2022.12.28.15.27.15; author bacon; state Exp; branches; next 1.10; commitid MJkRKemaqfXl1l7E; 1.10 date 2022.12.11.21.14.37; author bacon; state Exp; branches; next 1.9; commitid suwG512Rfjtsub5E; 1.9 date 2022.06.11.19.42.39; author bacon; state Exp; branches; next 1.8; commitid vpBeHA3UKTFqREHD; 1.8 date 2022.03.15.21.06.32; author bacon; state Exp; branches; next 1.7; commitid nQG9KwhSTSnc9mwD; 1.7 date 2021.12.14.18.58.56; author bacon; state Exp; branches; next 1.6; commitid uVxXMhZDvs1AmEkD; 1.6 date 2021.09.18.00.42.39; author bacon; state Exp; branches; next 1.5; commitid GvOqx5f52xbl6n9D; 1.5 date 2021.09.03.01.53.52; author bacon; state Exp; branches; next 1.4; commitid lg6pwTiWGM0qYr7D; 1.4 date 2021.08.28.18.34.37; author bacon; state Exp; branches; next 1.3; commitid ip3DCgeYFQhfIL6D; 1.3 date 2021.06.15.13.47.46; author bacon; state Exp; branches; next 1.2; commitid 7V6uFR7TgpigveXC; 1.2 date 2021.06.11.17.04.55; author bacon; state Exp; branches; next 1.1; commitid OcsSeKWwMbyNHJWC; 1.1 date 2021.03.24.15.20.08; author bacon; state Exp; branches; next ; commitid ZjpuC4YcbuCvGzMC; desc @@ 1.14 log @biology/biolibc: Update to 0.2.6 Updates for libxtend 0.2.0 API Add full list of functions to biolibc(3) man page Other documentation improvements Changes: https://github.com/auerlab/biolibc/releases @ text @# $NetBSD$ DISTNAME= biolibc-0.2.6 CATEGORIES= biology MASTER_SITES= ${MASTER_SITE_GITHUB:=auerlab/} OWNER= bacon@@NetBSD.org 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 MANDIR=${PREFIX}/${PKGMANDIR} pre-build: cd ${WRKSRC} && ${MAKE} PREFIX=${PREFIX} depend .include "../../devel/libxtend/buildlink3.mk" .include "../../mk/bsd.pkg.mk" @ 1.13 log @biology/biolibc: Update to 0.2.5 Make header files C++ compatible (extern C) bl_chrom_name_cmp(): Support names with embedded digits, e.g. chr2p bl_gff_extract_attribute(): Improve performance gff -> gff3 to distinguish from past and future GFF specs Silence some compiler warnings Changes: https://github.com/auerlab/biolibc/releases @ text @d3 1 a3 1 DISTNAME= biolibc-0.2.5 @ 1.12 log @biology/biolibc: Update to 0.2.4.3 Add extern "C" to support use from C++ apps @ text @d3 1 a3 1 DISTNAME= biolibc-0.2.4.3 a5 1 GITHUB_TAG= 3dc616d0903a024cb48f5f646680edf62c9eeeb1 @ 1.11 log @Change MAINTAINER= to OWNER= on mission-critical packages @ text @d1 1 a1 1 # $NetBSD: Makefile,v 1.10 2022/12/11 21:14:37 bacon Exp $ d3 1 a3 1 DISTNAME= biolibc-0.2.4 d6 1 @ 1.10 log @biology/biolibc: Update to 0.2.4 Minor enhancements Changes: https://github.com/auerlab/biolibc/releases @ text @d1 1 a1 1 # $NetBSD$ d7 1 a7 1 MAINTAINER= bacon@@NetBSD.org @ 1.9 log @biology/biolibc: Update to 0.2.3 Expand use of tsv_read_field_malloc() to improve memory efficiency Add SAM bit flag constants Import SAM-GFF compare functions from diffanal Updates for libxtend DSV API changes Numerous minor bug fixes and enhancements Changes: https://github.com/auerlab/biolibc/releases @ text @d3 1 a3 1 DISTNAME= biolibc-0.2.3 @ 1.8 log @biology/biolibc: Update to 0.2.2 Numerous bug fixes and enhancements Serveral new functions 3 new classes Cleaned up some API slop Changes: https://github.com/auerlab/biolibc/tags @ text @d3 1 a3 1 DISTNAME= biolibc-0.2.2 @ 1.7 log @biology/biolibc: Update to 0.2.1 Add orf.c with start/stop codon locators Standardize BED and GFF APIs Implement VCF input filtering Eliminate mutator macros mirroring mutator functions Numerous minor bug fixes and enhancements Changes: https://github.com/auerlab/biolibc/releases/tag/0.2.1 @ text @d3 1 a3 1 DISTNAME= biolibc-0.2.1 @ 1.6 log @biology/biolibc: Update to 0.2.0.11 Regenerate man pages with improved auto-c2man Improved formatting and added missing return value sections @ text @d3 1 a3 1 DISTNAME= biolibc-0.2.0.11 a5 1 GITHUB_TAG= 65b3b132c813bb04b3a9886d08f51af8137a60e6 a18 1 PLIST.cs= yes a21 1 PLIST_VARS= cs @ 1.5 log @biology/biolibc: Update to 0.2.0.1 Fix regression: Replace BL_BED_SET_STRAND() macro with bl_bed_set_strand(), which performs sanity checks @ text @d3 1 a3 1 DISTNAME= biolibc-0.2.0.1 d6 1 a6 1 GITHUB_TAG= f6de6e02d75bc6298c0885e45176b3b9c7f84c29 @ 1.4 log @biology/biolibc: Update to 0.2.0 Major API overhaul New classes for FASTA and FASTQ Generate accessor and mutator functions for all classes Generate man pages for all functions and macros Export delimiter-separated-value class to libxtend @ text @d3 1 a3 1 DISTNAME= biolibc-0.2.0 d6 1 @ 1.3 log @biology/biolibc: Update to 0.1.3.2 Add LDFLAGS to allow RELRO @ text @d3 1 a3 1 DISTNAME= biolibc-0.1.3.2 a5 1 GITHUB_TAG= 69d937861329b1842778d98091e65b3c3c624add d19 1 d22 2 a23 1 MAKE_ENV+= DYLIB_PATH=${PREFIX}/lib @ 1.2 log @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 @ text @d3 1 a3 1 DISTNAME= biolibc-0.1.3 d6 1 @ 1.1 log @biology/biolibc: import biolibc-0.1.1 Biolibc is a library of fast, memory-efficient, low-level functions for processing biological data. Like libc, it consists of numerous disparate, general-purpose functions which could be used by a wide variety of applications. These include functions for streaming common file formats such as SAM and VCF, string functions specific to bioinformatics, etc. @ text @d3 1 a3 1 DISTNAME= biolibc-0.1.1 d12 15 @