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pkgsrc/biology/sra-tools/PLIST
bacon c40bafe7ed biology/sra-tools: NCBI's toolkit for SRA 
SRA tools is a toolkit for using data in the INSDC Sequence Read
Archives.  SRAs operated by the International Nucleotide Sequence
Database Collaboration house sequence reads and alignments generated
by "next-gen" sequencers.  SRA tools allows conversion of .sra
files, which INSDC SRAs maintain, from/to other formats that the
'next-gen' sequencers generate including:

* csfasta/csqual (ABI SOLiD)
* fastq (and fasta for writing)
* hdf5 (PacBio, reading only)
* qseq (older Illumina)
* sam (writing only) / bam (reading only)
* sff

The toolkit uses the NCBI-VDB back-end enabling seamless access to
remote SRA data and local SRA files.
2023-08-29 00:00:24 +00:00

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@comment $NetBSD: PLIST,v 1.1 2023/08/29 00:00:24 bacon Exp $
bin/abi-dump
bin/abi-dump.3
bin/abi-dump.${PKGVERSION}
bin/align-info
bin/align-info.3
bin/align-info.${PKGVERSION}
bin/cache-mgr
bin/cache-mgr.3
bin/cache-mgr.${PKGVERSION}
bin/check-corrupt
bin/check-corrupt.3
bin/check-corrupt.${PKGVERSION}
bin/fasterq-dump
bin/fasterq-dump-orig.${PKGVERSION}
bin/fasterq-dump.3
bin/fasterq-dump.${PKGVERSION}
bin/fastq-dump
bin/fastq-dump-orig.${PKGVERSION}
bin/fastq-dump.3
bin/fastq-dump.${PKGVERSION}
bin/illumina-dump
bin/illumina-dump.3
bin/illumina-dump.${PKGVERSION}
bin/kdbmeta
bin/kdbmeta.3
bin/kdbmeta.${PKGVERSION}
bin/ngs-pileup
bin/ngs-pileup.3
bin/ngs-pileup.${PKGVERSION}
bin/prefetch
bin/prefetch-orig.${PKGVERSION}
bin/prefetch.3
bin/prefetch.${PKGVERSION}
bin/rcexplain
bin/rcexplain.3
bin/rcexplain.${PKGVERSION}
bin/ref-variation
bin/ref-variation.3
bin/ref-variation.${PKGVERSION}
bin/sam-dump
bin/sam-dump-orig.${PKGVERSION}
bin/sam-dump.3
bin/sam-dump.${PKGVERSION}
bin/sff-dump
bin/sff-dump.3
bin/sff-dump.${PKGVERSION}
bin/sra-info
bin/sra-info.3
bin/sra-info.${PKGVERSION}
bin/sra-pileup
bin/sra-pileup-orig.${PKGVERSION}
bin/sra-pileup.3
bin/sra-pileup.${PKGVERSION}
bin/sra-search
bin/sra-search.3
bin/sra-search.${PKGVERSION}
bin/sra-stat
bin/sra-stat.3
bin/sra-stat.${PKGVERSION}
bin/srapath
bin/srapath-orig.${PKGVERSION}
bin/srapath.3
bin/srapath.${PKGVERSION}
bin/sratools
bin/sratools.3
bin/sratools.${PKGVERSION}
bin/test-sra
bin/test-sra.3
bin/test-sra.${PKGVERSION}
bin/var-expand
bin/var-expand.3
bin/var-expand.${PKGVERSION}
bin/vdb-config
bin/vdb-config.3
bin/vdb-config.${PKGVERSION}
bin/vdb-decrypt
bin/vdb-decrypt.3
bin/vdb-decrypt.${PKGVERSION}
bin/vdb-dump
bin/vdb-dump-orig.${PKGVERSION}
bin/vdb-dump.3
bin/vdb-dump.${PKGVERSION}
bin/vdb-encrypt
bin/vdb-encrypt.3
bin/vdb-encrypt.${PKGVERSION}
bin/vdb-validate
bin/vdb-validate.3
bin/vdb-validate.${PKGVERSION}
include/ncbi-vdb/NGS.hpp
include/ngs/Alignment.hpp
include/ngs/AlignmentIterator.hpp
include/ngs/ErrorMsg.hpp
include/ngs/Fragment.hpp
include/ngs/FragmentIterator.hpp
include/ngs/Package.hpp
include/ngs/Pileup.hpp
include/ngs/PileupEvent.hpp
include/ngs/PileupEventIterator.hpp
include/ngs/PileupIterator.hpp
include/ngs/Read.hpp
include/ngs/ReadCollection.hpp
include/ngs/ReadGroup.hpp
include/ngs/ReadGroupIterator.hpp
include/ngs/ReadIterator.hpp
include/ngs/Reference.hpp
include/ngs/ReferenceIterator.hpp
include/ngs/ReferenceSequence.hpp
include/ngs/Statistics.hpp
include/ngs/StringRef.hpp
include/ngs/adapter/AlignmentItf.hpp
include/ngs/adapter/ErrorMsg.hpp
include/ngs/adapter/FragmentItf.hpp
include/ngs/adapter/PileupEventItf.hpp
include/ngs/adapter/PileupItf.hpp
include/ngs/adapter/ReadCollectionItf.hpp
include/ngs/adapter/ReadGroupItf.hpp
include/ngs/adapter/ReadItf.hpp
include/ngs/adapter/Refcount.hpp
include/ngs/adapter/ReferenceItf.hpp
include/ngs/adapter/ReferenceSequenceItf.hpp
include/ngs/adapter/StatisticsItf.hpp
include/ngs/adapter/StringItf.hpp
include/ngs/adapter/defs.h
include/ngs/inl/Alignment.hpp
include/ngs/inl/AlignmentIterator.hpp
include/ngs/inl/Fragment.hpp
include/ngs/inl/FragmentIterator.hpp
include/ngs/inl/Package.hpp
include/ngs/inl/Pileup.hpp
include/ngs/inl/PileupEvent.hpp
include/ngs/inl/PileupEventIterator.hpp
include/ngs/inl/PileupIterator.hpp
include/ngs/inl/Read.hpp
include/ngs/inl/ReadCollection.hpp
include/ngs/inl/ReadGroup.hpp
include/ngs/inl/ReadGroupIterator.hpp
include/ngs/inl/ReadIterator.hpp
include/ngs/inl/Reference.hpp
include/ngs/inl/ReferenceIterator.hpp
include/ngs/inl/ReferenceSequence.hpp
include/ngs/inl/Statistics.hpp
include/ngs/inl/StringRef.hpp
include/ngs/itf/AlignmentItf.h
include/ngs/itf/AlignmentItf.hpp
include/ngs/itf/ErrBlock.h
include/ngs/itf/ErrBlock.hpp
include/ngs/itf/ErrorMsg.hpp
include/ngs/itf/FragmentItf.h
include/ngs/itf/FragmentItf.hpp
include/ngs/itf/PackageItf.hpp
include/ngs/itf/PileupEventItf.h
include/ngs/itf/PileupEventItf.hpp
include/ngs/itf/PileupItf.h
include/ngs/itf/PileupItf.hpp
include/ngs/itf/ReadCollectionItf.h
include/ngs/itf/ReadCollectionItf.hpp
include/ngs/itf/ReadGroupItf.h
include/ngs/itf/ReadGroupItf.hpp
include/ngs/itf/ReadItf.h
include/ngs/itf/ReadItf.hpp
include/ngs/itf/Refcount.h
include/ngs/itf/Refcount.hpp
include/ngs/itf/ReferenceItf.h
include/ngs/itf/ReferenceItf.hpp
include/ngs/itf/ReferenceSequenceItf.h
include/ngs/itf/ReferenceSequenceItf.hpp
include/ngs/itf/StatisticsItf.h
include/ngs/itf/StatisticsItf.hpp
include/ngs/itf/StringItf.h
include/ngs/itf/StringItf.hpp
include/ngs/itf/VTable.h
include/ngs/itf/VTable.hpp
include/ngs/itf/defs.h
include/ngs/unix/arm64/atomic32.h
include/ngs/unix/fat86/atomic32.h
include/ngs/unix/i386/atomic32.h
include/ngs/unix/x86_64/atomic32.h
include/ngs/win/atomic32.h
include/ngs/win/stdbool.h
lib/libncbi-ngs-c++-static.a
lib/libncbi-ngs-c++.a
lib/libncbi-ngs-c++.a.3
lib/libncbi-ngs-c++.a.${PKGVERSION}
lib/libncbi-ngs-static.a
lib/libncbi-ngs.a
lib/libncbi-ngs.a.3
lib/libncbi-ngs.a.${PKGVERSION}
lib/libncbi-ngs.so
lib/libncbi-ngs.so.3
lib/libncbi-ngs.so.${PKGVERSION}
lib/libngs-c++-static.a
lib/libngs-c++.a
lib/libngs-c++.a.3
lib/libngs-c++.a.${PKGVERSION}
lib/libngs-c++.so
lib/libngs-c++.so.3
lib/libngs-c++.so.${PKGVERSION}
share/examples/sra-tools/AlignSliceTest.cpp
share/examples/sra-tools/AlignTest.cpp
share/examples/sra-tools/DumpReferenceFASTA.cpp
share/examples/sra-tools/FragTest.cpp
share/examples/sra-tools/Makefile
share/examples/sra-tools/PileupTest.cpp
share/examples/sra-tools/README.txt
share/examples/sra-tools/RefTest.cpp
share/examples/sra-tools/expected.txt
share/examples/sra-tools/python/AlignSliceTest.py
share/examples/sra-tools/python/AlignTest.py
share/examples/sra-tools/python/FragTest.py
share/examples/sra-tools/python/Makefile
share/examples/sra-tools/python/PileupTest.py
share/examples/sra-tools/python/README.txt
share/examples/sra-tools/python/RefTest.py
share/examples/sra-tools/python/expected.txt
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