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Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.
A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. JELLYFISH can count k-mers quickly by using an efficient encoding of a hash table and by exploiting the "compare-and-swap" CPU instruction to increase parallelism. WWW: http://www.genome.umd.edu/jellyfish.html PR: 207929 Submitted by: bacon4000@gmail.com
This commit is contained in:
Dmitry Marakasov
parent
b72580f6d4
commit
ee6e0c4336
Notes:
svn2git
2021-03-31 03:12:20 +00:00
svn path=/head/; revision=411785
@ -38,6 +38,7 @@
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SUBDIR += htslib
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SUBDIR += iolib
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SUBDIR += jalview
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SUBDIR += jellyfish
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SUBDIR += lagan
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SUBDIR += lamarc
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SUBDIR += libgtextutils
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46
biology/jellyfish/Makefile
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46
biology/jellyfish/Makefile
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# Created by: Jason Bacon <bacon4000@gmail.com>
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# $FreeBSD$
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PORTNAME= jellyfish
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PORTVERSION= 2.2.4
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DISTVERSIONPREFIX= v
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CATEGORIES= biology
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MAINTAINER= bacon4000@gmail.com
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COMMENT= Fast, memory-efficient counting of k-mers in DNA
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LICENSE= GPLv3+
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LICENSE_FILE= ${WRKSRC}/LICENSE
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BUILD_DEPENDS= yaggo:${PORTSDIR}/devel/yaggo
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GNU_CONFIGURE= yes
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USES= autoreconf compiler:c++11-lib gmake \
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libtool pkgconfig
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USE_LDCONFIG= yes
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USE_GITHUB= yes
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GH_ACCOUNT= gmarcais
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GH_PROJECT= Jellyfish
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INSTALL_TARGET= install-strip
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.include <bsd.port.pre.mk>
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# SSE code assumes amd64 features
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.if ${ARCH} != "amd64"
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.if ${OSVERSION} < 1000000
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IGNORE= multiple code issues on i386 < 10.0-RELEASE
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.else
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CONFIGURE_ARGS+=--without-sse
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.endif
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.endif
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# configure does not support --with-pkgconfigdir
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post-patch:
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@${REINPLACE_CMD} \
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-e 's|$$(libdir)/pkgconfig|${PREFIX}/libdata/pkgconfig|g' \
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${WRKSRC}/Makefile.am
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.include <bsd.port.post.mk>
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2
biology/jellyfish/distinfo
Normal file
2
biology/jellyfish/distinfo
Normal file
@ -0,0 +1,2 @@
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SHA256 (gmarcais-Jellyfish-v2.2.4_GH0.tar.gz) = 44b6478aed63b859b8287d72b4f9bfb5d513fed334efbc8a9e5783da12ecb3ec
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SIZE (gmarcais-Jellyfish-v2.2.4_GH0.tar.gz) = 658653
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@ -0,0 +1,35 @@
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--- include/jellyfish/file_header.hpp.orig 2015-10-27 14:32:31 UTC
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+++ include/jellyfish/file_header.hpp
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@@ -21,6 +21,8 @@
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#include <jellyfish/generic_file_header.hpp>
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#include <jellyfish/rectangular_binary_matrix.hpp>
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+using std::string;
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+
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namespace jellyfish {
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/// A header with jellyfish hash specific entries: size, matrix, etc.
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class file_header : public generic_file_header {
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@@ -42,7 +44,10 @@ public:
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RectangularBinaryMatrix matrix(int i = 1) const {
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std::string name("matrix");
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- name += std::to_string((long long int)i); // Cast to make gcc4.4 happy!
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+ char buff[100];
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+ // name += std::to_string((long long int)i); // Cast to make gcc4.4 happy!
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+ snprintf(buff, 99, "%d", i);
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+ name += buff;
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const unsigned int r = root_[name]["r"].asUInt();
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const unsigned int c = root_[name]["c"].asUInt();
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std::vector<uint64_t> raw(c, (uint64_t)0);
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@@ -53,7 +58,10 @@ public:
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void matrix(const RectangularBinaryMatrix& m, int i = 1) {
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std::string name("matrix");
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- name += std::to_string((long long int)i);
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+ char buff[100];
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+ // name += std::to_string((long long int)i);
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+ snprintf(buff, 99, "%d", i);
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+ name += buff;
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root_[name].clear();
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root_[name]["r"] = m.r();
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root_[name]["c"] = m.c();
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7
biology/jellyfish/pkg-descr
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7
biology/jellyfish/pkg-descr
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Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.
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A k-mer is a substring of length k, and counting the occurrences of all such
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substrings is a central step in many analyses of DNA sequence. JELLYFISH can
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count k-mers quickly by using an efficient encoding of a hash table and by
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exploiting the "compare-and-swap" CPU instruction to increase parallelism.
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WWW: http://www.genome.umd.edu/jellyfish.html
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55
biology/jellyfish/pkg-plist
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55
biology/jellyfish/pkg-plist
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@ -0,0 +1,55 @@
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bin/jellyfish
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include/jellyfish-2.2.4/jellyfish/allocators_mmap.hpp
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include/jellyfish-2.2.4/jellyfish/atomic_bits_array.hpp
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include/jellyfish-2.2.4/jellyfish/atomic_field.hpp
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include/jellyfish-2.2.4/jellyfish/atomic_gcc.hpp
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include/jellyfish-2.2.4/jellyfish/backtrace.hpp
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include/jellyfish-2.2.4/jellyfish/binary_dumper.hpp
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include/jellyfish-2.2.4/jellyfish/bloom_common.hpp
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include/jellyfish-2.2.4/jellyfish/bloom_counter2.hpp
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include/jellyfish-2.2.4/jellyfish/bloom_filter.hpp
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include/jellyfish-2.2.4/jellyfish/circular_buffer.hpp
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include/jellyfish-2.2.4/jellyfish/compare_and_swap.hpp
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include/jellyfish-2.2.4/jellyfish/cooperative_pool.hpp
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include/jellyfish-2.2.4/jellyfish/cooperative_pool2.hpp
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include/jellyfish-2.2.4/jellyfish/cpp_array.hpp
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include/jellyfish-2.2.4/jellyfish/divisor.hpp
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include/jellyfish-2.2.4/jellyfish/dumper.hpp
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include/jellyfish-2.2.4/jellyfish/err.hpp
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include/jellyfish-2.2.4/jellyfish/file_header.hpp
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include/jellyfish-2.2.4/jellyfish/generator_manager.hpp
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include/jellyfish-2.2.4/jellyfish/generic_file_header.hpp
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include/jellyfish-2.2.4/jellyfish/hash_counter.hpp
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include/jellyfish-2.2.4/jellyfish/int128.hpp
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include/jellyfish-2.2.4/jellyfish/jellyfish.hpp
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include/jellyfish-2.2.4/jellyfish/json.h
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include/jellyfish-2.2.4/jellyfish/large_hash_array.hpp
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include/jellyfish-2.2.4/jellyfish/large_hash_iterator.hpp
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include/jellyfish-2.2.4/jellyfish/locks_pthread.hpp
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include/jellyfish-2.2.4/jellyfish/mapped_file.hpp
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include/jellyfish-2.2.4/jellyfish/mer_dna.hpp
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include/jellyfish-2.2.4/jellyfish/mer_dna_bloom_counter.hpp
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include/jellyfish-2.2.4/jellyfish/mer_heap.hpp
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include/jellyfish-2.2.4/jellyfish/mer_iterator.hpp
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include/jellyfish-2.2.4/jellyfish/mer_overlap_sequence_parser.hpp
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include/jellyfish-2.2.4/jellyfish/mer_qual_iterator.hpp
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include/jellyfish-2.2.4/jellyfish/misc.hpp
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include/jellyfish-2.2.4/jellyfish/offsets_key_value.hpp
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include/jellyfish-2.2.4/jellyfish/rectangular_binary_matrix.hpp
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include/jellyfish-2.2.4/jellyfish/simple_circular_buffer.hpp
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include/jellyfish-2.2.4/jellyfish/sorted_dumper.hpp
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include/jellyfish-2.2.4/jellyfish/stdio_filebuf.hpp
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include/jellyfish-2.2.4/jellyfish/storage.hpp
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include/jellyfish-2.2.4/jellyfish/stream_iterator.hpp
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include/jellyfish-2.2.4/jellyfish/stream_manager.hpp
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include/jellyfish-2.2.4/jellyfish/text_dumper.hpp
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include/jellyfish-2.2.4/jellyfish/thread_exec.hpp
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include/jellyfish-2.2.4/jellyfish/time.hpp
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include/jellyfish-2.2.4/jellyfish/token_ring.hpp
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include/jellyfish-2.2.4/jellyfish/whole_sequence_parser.hpp
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lib/libjellyfish-2.0.a
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lib/libjellyfish-2.0.so
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lib/libjellyfish-2.0.so.2
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lib/libjellyfish-2.0.so.2.0.0
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libdata/pkgconfig/jellyfish-2.0.pc
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man/man1/jellyfish.1.gz
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