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biology/bifrost: Parallel tool for de Bruijn graphs
Bifrost is a tool and API for parallel construction, indexing and querying of colored and compacted de Bruijn graphs from FASTA/FASTQ DNA/RNA sequence files.
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Jason W. Bacon
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Jason W. Bacon
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Jul 7, 2023
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PORTNAME= bifrost | ||
DISTVERSIONPREFIX= v | ||
DISTVERSION= 1.2.1 | ||
CATEGORIES= biology | ||
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MAINTAINER= jwb@FreeBSD.org | ||
COMMENT= Parallel construction, indexing and querying of de Bruijn graphs | ||
WWW= https://github.com/pmelsted/bifrost | ||
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LICENSE= BSD2CLAUSE | ||
LICENSE_FILE= ${WRKSRC}/LICENSE | ||
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USES= cmake | ||
USE_GITHUB= yes | ||
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GH_ACCOUNT= pmelsted | ||
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.include <bsd.port.mk> |
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TIMESTAMP = 1688397139 | ||
SHA256 (pmelsted-bifrost-v1.2.1_GH0.tar.gz) = fe93080ef3ea71ff009fc206b5c17dd40fbfd18293000621a83d7d947dfedf1a | ||
SIZE (pmelsted-bifrost-v1.2.1_GH0.tar.gz) = 905438 |
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--- src/strict_fstream.hpp.orig 2023-07-03 15:14:36 UTC | ||
+++ src/strict_fstream.hpp | ||
@@ -64,7 +64,7 @@ static std::string strerror() | ||
} else { | ||
return "Unknown error (" + std::to_string(err_num) + ")"; | ||
} | ||
-#elif ((_POSIX_C_SOURCE >= 200112L || _XOPEN_SOURCE >= 600) && ! _GNU_SOURCE) || defined(__APPLE__) || defined(__MUSL__) | ||
+#elif ((_POSIX_C_SOURCE >= 200112L || _XOPEN_SOURCE >= 600) && ! _GNU_SOURCE) || defined(__APPLE__) || defined(__MUSL__) || defined(__FreeBSD__) | ||
// XSI-compliant strerror_r() | ||
const int err_num = errno; // See above | ||
if (strerror_r(err_num, buff.data(), buff.size()) == 0) { |
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Bifrost is a tool and API for parallel construction, indexing and | ||
querying of colored and compacted de Bruijn graphs from FASTA/FASTQ | ||
DNA/RNA sequence files. |
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bin/Bifrost | ||
include/bifrost/BitContainer.hpp | ||
include/bifrost/BlockedBloomFilter.hpp | ||
include/bifrost/ColorSet.hpp | ||
include/bifrost/ColoredCDBG.hpp | ||
include/bifrost/ColoredCDBG.tcc | ||
include/bifrost/Common.hpp | ||
include/bifrost/CompactedDBG.hpp | ||
include/bifrost/CompactedDBG.tcc | ||
include/bifrost/CompressedCoverage.hpp | ||
include/bifrost/CompressedSequence.hpp | ||
include/bifrost/DataAccessor.hpp | ||
include/bifrost/DataAccessor.tcc | ||
include/bifrost/DataManager.hpp | ||
include/bifrost/DataStorage.hpp | ||
include/bifrost/DataStorage.tcc | ||
include/bifrost/FASTX_Parser.hpp | ||
include/bifrost/File_Parser.hpp | ||
include/bifrost/GFA_Parser.hpp | ||
include/bifrost/IO.tcc | ||
include/bifrost/Kmer.hpp | ||
include/bifrost/KmerCovIndex.hpp | ||
include/bifrost/KmerCovIndex.tcc | ||
include/bifrost/KmerHashTable.hpp | ||
include/bifrost/KmerIterator.hpp | ||
include/bifrost/KmerStream.hpp | ||
include/bifrost/Lock.hpp | ||
include/bifrost/MinimizerIndex.hpp | ||
include/bifrost/NeighborIterator.hpp | ||
include/bifrost/NeighborIterator.tcc | ||
include/bifrost/RepHash.hpp | ||
include/bifrost/Search.tcc | ||
include/bifrost/StreamCounter.hpp | ||
include/bifrost/TinyBitmap.hpp | ||
include/bifrost/TinyVector.hpp | ||
include/bifrost/Unitig.hpp | ||
include/bifrost/UnitigIterator.hpp | ||
include/bifrost/UnitigIterator.tcc | ||
include/bifrost/UnitigMap.hpp | ||
include/bifrost/UnitigMap.tcc | ||
include/bifrost/getRSS.h | ||
include/bifrost/kseq.h | ||
include/bifrost/libdivide.h | ||
include/bifrost/libpopcnt.h | ||
include/bifrost/minHashIterator.hpp | ||
include/bifrost/roaring.h | ||
include/bifrost/roaring.hh | ||
include/bifrost/rw_spin_lock.h | ||
include/bifrost/strict_fstream.hpp | ||
include/bifrost/wyhash.h | ||
include/bifrost/zstr.hpp | ||
lib/libbifrost.a | ||
lib/libbifrost.so |