Import jellyfish-2.2.0 as wip/jellyfish2.
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.
This commit is contained in:
Jason Bacon
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6f3ade5810
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6 changed files with 160 additions and 0 deletions
5
jellyfish2/DESCR
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5
jellyfish2/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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59
jellyfish2/Makefile
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59
jellyfish2/Makefile
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# $NetBSD$
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#
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###########################################################
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# Generated by fbsd2pkg #
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###########################################################
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###########################################################
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# Unconverted and partially converted FreeBSD port syntax:
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## Created by: Jason Bacon <bacon4000@gmail.com>
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## $FreeBSD$
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#USE_LDCONFIG= yes
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#post-stage:
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# ${MV} ${DESTDIR}${PREFIX}/lib/pkgconfig/* \
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# ${DESTDIR}${PREFIX}/libdata/pkgconfig
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#.include <bsd.port.mk>
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DISTNAME= jellyfish-${PORTVERSION}
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CATEGORIES= biology
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MASTER_SITES= ftp://ftp.genome.umd.edu/pub/jellyfish/
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MAINTAINER= dsiercks@uwm.edu
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HOMEPAGE= http://www.genome.umd.edu/jellyfish.html
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COMMENT= Fast, memory-efficient counting of k-mers in DNA
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# Check this
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LICENSE= gnu-gpl-v3
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# FIXME: Only for amd64
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# Test and change if necessary.
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# MAKE_JOBS_SAFE= no
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# Just assuming C and C++: Adjust this!
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USE_LANGUAGES= c c++
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USE_LIBTOOL= yes
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GNU_CONFIGURE= yes
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CFLAGS= -fopenmp
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CXXFLAGS+= -std=c++0x
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FFLAGS= -fopenmp
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PORTVERSION= 2.2.0
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DATADIR= ${PREFIX}/share/jellyfish
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DOCSDIR= ${PREFIX}/share/doc/jellyfish
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# Sets OPSYS, OS_VERSION, MACHINE_ARCH, etc..
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# .include "../../mk/bsd.prefs.mk"
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# Keep this if there are user-selectable options.
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# .include "options.mk"
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# Specify which directories to create before install.
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# You should only need this if using your own install target.
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INSTALLATION_DIRS= bin lib ${PKGMANDIR}/man1 share/doc share/examples
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# Linux doesn't have zlib in the base, so just in case...
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# .include "../../devel/zlib/buildlink3.mk"
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.include "../../mk/bsd.pkg.mk"
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53
jellyfish2/PLIST
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53
jellyfish2/PLIST
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@comment $NetBSD$
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bin/jellyfish
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include/${PKGNAME}/jellyfish/allocators_mmap.hpp
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include/${PKGNAME}/jellyfish/atomic_bits_array.hpp
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include/${PKGNAME}/jellyfish/atomic_field.hpp
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include/${PKGNAME}/jellyfish/atomic_gcc.hpp
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include/${PKGNAME}/jellyfish/backtrace.hpp
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include/${PKGNAME}/jellyfish/binary_dumper.hpp
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include/${PKGNAME}/jellyfish/bloom_common.hpp
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include/${PKGNAME}/jellyfish/bloom_counter2.hpp
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include/${PKGNAME}/jellyfish/bloom_filter.hpp
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include/${PKGNAME}/jellyfish/circular_buffer.hpp
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include/${PKGNAME}/jellyfish/compare_and_swap.hpp
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include/${PKGNAME}/jellyfish/cooperative_pool2.hpp
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include/${PKGNAME}/jellyfish/cooperative_pool.hpp
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include/${PKGNAME}/jellyfish/cpp_array.hpp
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include/${PKGNAME}/jellyfish/divisor.hpp
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include/${PKGNAME}/jellyfish/dumper.hpp
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include/${PKGNAME}/jellyfish/err.hpp
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include/${PKGNAME}/jellyfish/file_header.hpp
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include/${PKGNAME}/jellyfish/generator_manager.hpp
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include/${PKGNAME}/jellyfish/generic_file_header.hpp
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include/${PKGNAME}/jellyfish/hash_counter.hpp
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include/${PKGNAME}/jellyfish/int128.hpp
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include/${PKGNAME}/jellyfish/jellyfish.hpp
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include/${PKGNAME}/jellyfish/json.h
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include/${PKGNAME}/jellyfish/large_hash_array.hpp
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include/${PKGNAME}/jellyfish/large_hash_iterator.hpp
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include/${PKGNAME}/jellyfish/locks_pthread.hpp
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include/${PKGNAME}/jellyfish/mapped_file.hpp
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include/${PKGNAME}/jellyfish/mer_dna_bloom_counter.hpp
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include/${PKGNAME}/jellyfish/mer_dna.hpp
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include/${PKGNAME}/jellyfish/mer_heap.hpp
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include/${PKGNAME}/jellyfish/mer_iterator.hpp
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include/${PKGNAME}/jellyfish/mer_overlap_sequence_parser.hpp
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include/${PKGNAME}/jellyfish/mer_qual_iterator.hpp
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include/${PKGNAME}/jellyfish/misc.hpp
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include/${PKGNAME}/jellyfish/offsets_key_value.hpp
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include/${PKGNAME}/jellyfish/rectangular_binary_matrix.hpp
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include/${PKGNAME}/jellyfish/simple_circular_buffer.hpp
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include/${PKGNAME}/jellyfish/sorted_dumper.hpp
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include/${PKGNAME}/jellyfish/stdio_filebuf.hpp
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include/${PKGNAME}/jellyfish/storage.hpp
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include/${PKGNAME}/jellyfish/stream_iterator.hpp
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include/${PKGNAME}/jellyfish/stream_manager.hpp
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include/${PKGNAME}/jellyfish/text_dumper.hpp
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include/${PKGNAME}/jellyfish/thread_exec.hpp
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include/${PKGNAME}/jellyfish/time.hpp
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include/${PKGNAME}/jellyfish/token_ring.hpp
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include/${PKGNAME}/jellyfish/whole_sequence_parser.hpp
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lib/libjellyfish-2.0.la
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lib/pkgconfig/jellyfish-2.0.pc
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man/man1/jellyfish.1
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1
jellyfish2/TODO
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1
jellyfish2/TODO
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Clean up and test.
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5
jellyfish2/distinfo
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5
jellyfish2/distinfo
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$NetBSD$
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SHA1 (jellyfish-2.2.0.tar.gz) = 9ac4817aed0c61a1819b913193b0e312fa4fa9bd
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RMD160 (jellyfish-2.2.0.tar.gz) = 01e5847c72bf1bf92989b1158988605b1155aec4
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Size (jellyfish-2.2.0.tar.gz) = 1085913 bytes
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37
jellyfish2/patches/patch-include_jellyfish_file__header.hpp
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jellyfish2/patches/patch-include_jellyfish_file__header.hpp
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$NetBSD$
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--- include/jellyfish/file_header.hpp.orig 2013-12-13 19:04:16 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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