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#ifndef _SEQUENCE_H_
#define _SEQUENCE_H_
/**
* WHAM - high-throughput sequence aligner
* Copyright (C) 2011 WHAM Group, University of Wisconsin
*
* This program 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 3 of the License, or
* (at your option) any later version.
*
* This program 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 this program. If not, see <http://www.gnu.org/licenses/>.
*/
/* $Id: sequence.h 157 2012-07-25 05:58:09Z yinan $ */
#include "lib.h"
#include <stdio.h>
#include "interval.h"
#define BASE_A 0
#define BASE_C 1
#define BASE_G 2
#define BASE_T 3
#define BASE_N 4
#define NUM_LONGWORD(x) ((((x) - 1) >> BITS_LONGWORD_SHIFT) + 1)
#define NUM_LONGWORD_BASE(x) (((((x) - 1) >> BITS_LONGWORD_SHIFT) * BITS_PER_BASE) + 1)
#define BITMAP_IS(x, y) (((x) >> (y)) & 0x1)
#define BITMAP_SET(x, y) ((x) |= (0x1 << (y)))
#define BITMAP_CLEAR(x, y) ((x) &= ~(0x1 << (y)))
#define MAX_NUM_CHAR 4294967295LLU
#define SEQUENCE_HEAD_WORDS 6
#define MAX_LENGTH_PATH 256
class Aligner;
class CompactSequence {
private:
uint32 numChar; /* the number of characters in the compact sequence */
uint32 numNSegment; /* the number of N segments */
uint32 size; /* the size of the compact sequence (3bit/character) */
int64 * sequence; /* the sequence (has an offset to the beginingn of the pool array) */
int64 * pool; /* the space for storing the compact sequence */
char ** seqNames; /* file names */
char * seqNamepool;
uint32 * seqLens;
int nSeq; /* the number of sequences */
int len;
int nError;
bool skipMask; /* treat the masks( lowercase characters) as unknown character)*/
uint32 numRead;
int64 * keys;
uint32 * offsets;
public:
IntervalTree * itree; /* the interval tree that used for translation between orginal sequence offset and compact sequence offset. */
public:
CompactSequence();
CompactSequence(bool skip);
int build(char ** fname, int numSeq, int length, int numError);
int filter(Aligner * aligner, char ** fname, int numFile, char * path);
int save(char * path);
int load(char * path);
int alignment(int lenKey, int nMismatch);
int valid(int length, int numError);
static void compose(char * str, int length, int64 * words);
static void decompose(char * str, int length, int64 * words);
private:
int preProcess(char * fname, uint32 numError, int64 & num,
int64 & numNSegment, int64 & numFileSeq);
int skipLine(FILE * file);
int getSeqName(FILE * file, char * str);
void extractFileName(char * dest, char * src);
public:
unsigned int getNum() {
return numChar;
}
int getNumSeq() {
return nSeq;
}
int64 * getSequence() {
return sequence;
}
char * getSeqName(int sid) {
return seqNames[sid];
}
uint32 getSeqLen(int sid) {
return seqLens[sid];
}
};
//CompactSequence * sequenceLoad(char * fname, int length);
#endif
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