Package: bedtools
Version: 2.30.0
Revision: 1
Description: Utilities for comparing genomic features
License: GPL
Maintainer: Hanspeter Niederstrasser <nieder@users.sourceforge.net>
Depends: <<
	bzip2-shlibs,
	liblzma5-shlibs
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BuildDepends: <<
	babel-py37,
	bzip2-dev,
	fink-package-precedence,
	liblzma5,
	pytz-py37,
	setuptools-tng-py37,
	sphinx-py37 (>= 1.2.2)
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Source: https://github.com/arq5x/bedtools2/releases/download/v%v/%n-%v.tar.gz
Source-Checksum: SHA256(333ad1ffcdc6e36005b4d6c9290677986ee97871cff92ed821c1b643d38150b8)
SourceDirectory: %n2
PatchScript: <<
	# uses internal patched copy of htslib, but we don't need to make the shared lib
	perl -pi -e 's|lib-static lib-shared|lib-static|g' src/utils/htslib/Makefile
<<
#PatchFile: %n.patch
#PatchFile-MD5: 8033216a91ea83a50d38e878762c2788
GCC: 4.0
#SetCPPFLAGS: -MD -I%p/include
#UseMaxBuildJobs: false
CompileScript: <<
	make -w CPPFLAGS="-MD -I%p/include" VERBOSE=1
	make -j1 -C docs man SPHINXBUILD=%p/bin/sphinx-build3.7
	make -j1 -C docs html SPHINXBUILD=%p/bin/sphinx-build3.7
	fink-package-precedence --depfile-ext='\.d' .
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InfoTest: <<
	TestDepends: samtools
	TestScript: make test || exit 2
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InstallScript: <<
	make install DESTDIR=%d prefix=%p
	install -m 755 -d %i/share/man/man1
	install -m 755 -d %i/share/doc/%n
	cp docs/_build/man/%n.1 %i/share/man/man1
	cp -R docs/_build/html %i/share/doc/%n
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DocFiles: LICENSE README.md
Homepage: https://github.com/arq5x/bedtools2
DescDetail: <<
The BEDTools utilities allow one to address common genomics tasks such as 
finding feature overlaps and computing coverage. The utilities are largely 
based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. 
Using BEDTools, one can develop sophisticated pipelines that answer 
complicated research questions by "streaming" several BEDTools together. 
The following are examples of common questions that one can address with 
BEDTools.

    Intersecting two BED files in search of overlapping features.
    Culling/refining/computing coverage for BAM alignments based on genome 
features.
    Merging overlapping features.
    Screening for paired-end (PE) overlaps between PE sequences and 
existing genomic features.
    Calculating the depth and breadth of sequence coverage across defined 
"windows" in a genome.
    Screening for overlaps between "split" alignments and genomic features.

Quinlan AR and Hall IM, 2010. BEDTools: a flexible suite of utilities for 
comparing genomic features. Bioinformatics. 26, 6, pp. 841-842.
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DescPackaging: <<
Xcode9 fix for strandqueue
https://github.com/arq5x/bedtools2/pull/574
<<