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Contents
/*
Copyright 2007, 2008, 2009 Daniel Zerbino (zerbino@ebi.ac.uk)
This file is part of Velvet.
Velvet is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
Velvet is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with Velvet; if not, write to the Free Software
Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
*/
#ifndef _KMER_H_
#define _KMER_H_
#include <stdint.h>
#include "globals.h"
void copyKmers(Kmer* k1, Kmer* k2);
void pushNucleotide(Kmer * kmer, Nucleotide nucleotide);
Nucleotide popNucleotide(Kmer * kmer);
int compareKmers(Kmer* k1, Kmer* k2);
void reversePushNucleotide(Kmer * kmer, Nucleotide nucleotide);
KmerKey getKmerKey(Kmer * kmer);
void printKmer(Kmer * kmer);
void clearKmer(Kmer * kmer);
void resetWordFilter(int wordLength);
void resetKeyFilter(int keyLength);
#define KMER_QUOTIENT (MAXKMERLENGTH / 4)
#define KMER_REMAINDER (MAXKMERLENGTH % 4)
#if KMER_REMAINDER
#define KMER_BYTE_SIZE (KMER_QUOTIENT + 1)
#else
#define KMER_BYTE_SIZE KMER_QUOTIENT
#endif
#define KMER_LONGLONGS (KMER_BYTE_SIZE / 8)
#define KMER_LONGS ((KMER_BYTE_SIZE % 8) / 4)
#define KMER_INTS ((KMER_BYTE_SIZE % 4) / 2)
#define KMER_CHARS (KMER_BYTE_SIZE % 2)
struct kmer_st {
#if KMER_LONGLONGS
uint64_t longlongs[KMER_LONGLONGS];
#endif
#if KMER_LONGS
uint32_t longs;
#endif
#if KMER_INTS
uint16_t ints;
#endif
#if KMER_CHARS
uint8_t chars;
#endif
} ATTRIBUTE_PACKED;
#endif
Version data entries
14 entries across 14 versions & 2 rubygems