biology/bedtools: Update to 2.31.1
Code updates for modern compilers Changes: https://github.com/arq5x/bedtools2/releases
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bacon
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The bedtools utilities are a suite of tools for performing a wide range of
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genomics analysis tasks. The most widely-used of these tools enable genome
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arithmetic, i.e., set theory on the genome. For example, with bedtools one
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can intersect, merge, count, complement, and shuffle genomic intervals from
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multiple files in common genomic formats such as BAM, BED, GFF/GTF, and VCF.
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The bedtools utilities are a suite of tools for performing a wide
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range of genomics analysis tasks. The most widely-used of these
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tools enable genome arithmetic, i.e., set theory on the genome.
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For example, with bedtools one can intersect, merge, count,
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complement, and shuffle genomic intervals from multiple files in
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common genomic formats such as BAM, BED, GFF/GTF, and VCF.
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Although each individual utility is designed to do a relatively simple task,
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e.g., intersect two interval files, more sophisticated analyses can be
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conducted by stringing together multiple bedtools operations on the command
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line or in shell scripts.
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Although each individual utility is designed to do a relatively
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simple task, e.g., intersect two interval files, more sophisticated
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analyses can be conducted by stringing together multiple bedtools
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operations on the command line or in shell scripts.
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@ -1,13 +1,12 @@
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# $NetBSD: Makefile,v 1.5 2023/08/14 05:23:51 wiz Exp $
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# $NetBSD: Makefile,v 1.6 2023/11/08 16:46:44 bacon Exp $
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DISTNAME= bedtools-2.30.0
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PKGREVISION= 2
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DISTNAME= bedtools-2.31.1
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CATEGORIES= biology
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MASTER_SITES= ${MASTER_SITE_GITHUB:=arq5x/}
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GITHUB_PROJECT= bedtools2
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GITHUB_TAG= v${PKGVERSION_NOREV}
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MAINTAINER= bacon@NetBSD.org
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OWNER= bacon@NetBSD.org
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HOMEPAGE= https://bedtools.readthedocs.io/en/latest/
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COMMENT= Swiss army knife for genome arithmetic
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LICENSE= mit
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@ -17,13 +16,13 @@ USE_TOOLS+= bash:test gmake
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REPLACE_SH+= scripts/vcfsort.sh
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REPLACE_PYTHON= scripts/makeBashScripts.py
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LDFLAGS.SunOS+= -lsocket
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SUBST_CLASSES+= pybin
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SUBST_STAGE.pybin= pre-configure
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SUBST_SED.pybin= -e 's|python|${PYTHONBIN}|g'
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SUBST_FILES.pybin= Makefile
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LDFLAGS.SunOS+= -lsocket
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do-test:
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cd ${WRKSRC}/test && bash test.sh
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@ -1,9 +1,9 @@
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$NetBSD: distinfo,v 1.4 2021/10/26 10:03:37 nia Exp $
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$NetBSD: distinfo,v 1.5 2023/11/08 16:46:44 bacon Exp $
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BLAKE2s (bedtools-2.30.0.tar.gz) = f4e0cdb0d7ca32da2724c1afcf707c02a02ab201b66b93e4ce26d9a51e0566c5
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SHA512 (bedtools-2.30.0.tar.gz) = 3d69d6a53d3e5d15597dfefa26f7895231adbf3c1fe3b16ee4213e497ef01a20698add2f0e6f03d8eb7cd7c70709955f0ebdf897a025a83d31ef17e2c91f9856
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Size (bedtools-2.30.0.tar.gz) = 20639858 bytes
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SHA1 (patch-Makefile) = d21b4a69ce18eac7de59d277a03d0a5f5e2e1cb5
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BLAKE2s (bedtools-2.31.1.tar.gz) = e5b3faf919f7aaf12251b29fa248e85248ec30dadab45c3fd23523d7ddc78c05
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SHA512 (bedtools-2.31.1.tar.gz) = b62feeb6ef211314a86e022b6104cc2291086b940913cff5878759c37a8be0ac50c174020d8555d71dbc29e6be56ea40fc3c6543b5ef444bc7535124814688d6
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Size (bedtools-2.31.1.tar.gz) = 21085970 bytes
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SHA1 (patch-Makefile) = f38634cad79026c0dd0cad6a6a70db933f002d5f
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SHA1 (patch-src_utils_BamTools_include_SamHeader.hpp) = 7ab168b247b5edf7f3eccd9ef7329a5e1605c787
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SHA1 (patch-src_utils_htslib_Makefile) = 8785ff3110f8df26e0cc5b2fdf1e2e02d6cdc836
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SHA1 (patch-test_test.sh) = e3a17815d6a30c17db7134613d25f08c6be3494e
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@ -1,8 +1,8 @@
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$NetBSD: patch-Makefile,v 1.2 2021/02/08 01:49:25 bacon Exp $
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$NetBSD: patch-Makefile,v 1.3 2023/11/08 16:46:44 bacon Exp $
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# Respect pkgsrc env, drop bash dep
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# Portability, respect env
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--- Makefile.orig 2021-02-05 21:42:03.926301547 +0000
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--- Makefile.orig 2023-11-08 15:05:30.454330622 +0000
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+++ Makefile
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@@ -4,7 +4,7 @@
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# (c) 2009 Aaron Quinlan
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@ -20,9 +20,9 @@ $NetBSD: patch-Makefile,v 1.2 2021/02/08 01:49:25 bacon Exp $
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-CXX = g++
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+CXX ?= g++
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ifeq ($(DEBUG),1)
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BT_CPPFLAGS = -DDEBUG -D_DEBUG -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API $(INCLUDES)
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@@ -41,7 +41,7 @@ endif
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PYTHON ?= $(shell python --version >/dev/null 2>&1 && echo "python" || echo python3)
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@@ -43,7 +43,7 @@ endif
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BT_LDFLAGS =
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BT_LIBS = -lz -lm -lbz2 -llzma -lpthread
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@ -31,16 +31,16 @@ $NetBSD: patch-Makefile,v 1.2 2021/02/08 01:49:25 bacon Exp $
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SUBDIRS = $(SRC_DIR)/annotateBed \
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$(SRC_DIR)/bamToBed \
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@@ -155,7 +155,7 @@ $(CCPREFIX) $(CC_WRAPPER) $(CXX) $(ALL_C
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@@ -158,7 +158,7 @@ $(CCPREFIX) $(CC_WRAPPER) $(CXX) $(ALL_C
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@mv -f $*.Td $*.d
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endef
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-$(OBJ_DIR)/%.d: ;
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+$(OBJ_DIR)/%.d: $(OBJ_DIR) ;
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+$(OBJ_DIR)/%.d: $(OBJ_DIR);
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.PRECIOUS: $(OBJ_DIR)/%.d
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-include $(patsubst %.o,%.d,$(BUILT_OBJECTS))
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@@ -197,9 +197,9 @@ $(BIN_DIR)/intersectBed: | $(BIN_DIR)
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@@ -200,9 +200,9 @@ $(BIN_DIR)/intersectBed: | $(BIN_DIR)
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.PHONY: all
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install: all
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