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/*
* ReadsProcessor.cpp
* Contains methods for formatting sequences to place into bloom filter
* For memory management purposes the kmer is intermediately stored here.
*
* Created on: Aug 8, 2012
* Author: cjustin
*/
#include "ReadsProcessor.h"
#include <cassert>
#include <iostream>
#include <cstring>
#include <sstream>
//@todo: decide on endian convention for kmers, currently assuming little endian for ease of bitshifts
/*
* Needed for use of optimized char* returning prepSeq
*/
ReadsProcessor::ReadsProcessor(unsigned windowSize) :
m_kmerSize(windowSize), m_kmerSizeInBytes(windowSize / 4), m_halfSizeOfKmerInBytes(
windowSize / 8), m_hangingBases(0), m_hangingBasesExist(0)
{
//parsing code require kmer larger than 3
assert(m_kmerSize > 3);
if (windowSize % 8 != 0) {
m_halfSizeOfKmerInBytes++;
m_hangingBases = windowSize % 4;
if (m_hangingBases % 4 != 0) {
m_kmerSizeInBytes++;
m_hangingBasesExist = 1;
}
}
m_fw = new unsigned char[m_kmerSizeInBytes];
m_rv = new unsigned char[m_kmerSizeInBytes];
}
static const uint8_t fw3[256] = {
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //0
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //1
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //2
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //3
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0x00, 0xFF, 0x01, 0xFF, 0xFF, 0xFF, 0x02, //4 A C G
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0x03, 0xFF, 0xFF, 0xFF, //5 T
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0x00, 0xFF, 0x01, 0xFF, 0xFF, 0xFF, 0x02, //6 a c g
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0x03, 0xFF, 0xFF, 0xFF, //7 t
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //8
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //9
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //A
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //B
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //C
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //D
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //E
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //F
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF
};
static const uint8_t fw2[256] = {
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //0
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //1
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //2
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //3
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0x00, 0xFF, 0x04, 0xFF, 0xFF, 0xFF, 0x08, //4 A C G
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0x0C, 0xFF, 0xFF, 0xFF, //5 T
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0x00, 0xFF, 0x04, 0xFF, 0xFF, 0xFF, 0x08, //6 a c g
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0x0C, 0xFF, 0xFF, 0xFF, //7 t
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //8
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //9
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //A
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //B
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //C
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //D
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //E
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //F
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF
};
static const uint8_t fw1[256] = {
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //0
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //1
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //2
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //3
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0x00, 0xFF, 0x10, 0xFF, 0xFF, 0xFF, 0x20, //4 A C G
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0x30, 0xFF, 0xFF, 0xFF, //5 T
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0x00, 0xFF, 0x10, 0xFF, 0xFF, 0xFF, 0x20, //6 a c g
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0x30, 0xFF, 0xFF, 0xFF, //7 t
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //8
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //9
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //A
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //B
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //C
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //D
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //E
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //F
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF
};
static const uint8_t fw0[256] = {
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //0
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //1
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //2
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //3
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0x00, 0xFF, 0x40, 0xFF, 0xFF, 0xFF, 0x80, //4 A C G
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xC0, 0xFF, 0xFF, 0xFF, //5 T
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0x00, 0xFF, 0x40, 0xFF, 0xFF, 0xFF, 0x80, //6 a c g
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xC0, 0xFF, 0xFF, 0xFF, //7 t
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //8
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //9
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //A
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //B
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //C
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //D
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //E
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //F
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF
};
static const uint8_t rv3[256] = {
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //0
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //1
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //2
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //3
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0x03, 0xFF, 0x02, 0xFF, 0xFF, 0xFF, 0x01, //4 A C G
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0x00, 0xFF, 0xFF, 0xFF, //5 T
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0x03, 0xFF, 0x02, 0xFF, 0xFF, 0xFF, 0x01, //6 a c g
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0x00, 0xFF, 0xFF, 0xFF, //7 t
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //8
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //9
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //A
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //B
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //C
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //D
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //E
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //F
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF
};
static const uint8_t rv2[256] = {
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //0
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //1
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //2
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //3
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0x0C, 0xFF, 0x08, 0xFF, 0xFF, 0xFF, 0x04, //4 A C G
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0x00, 0xFF, 0xFF, 0xFF, //5 T
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0x0C, 0xFF, 0x08, 0xFF, 0xFF, 0xFF, 0x04, //6 a c g
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0x00, 0xFF, 0xFF, 0xFF, //7 t
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //8
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //9
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //A
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //B
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //C
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //D
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //E
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //F
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF
};
static const uint8_t rv1[256] = {
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //0
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //1
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //2
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //3
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0x30, 0xFF, 0x20, 0xFF, 0xFF, 0xFF, 0x10, //4 A C G
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0x00, 0xFF, 0xFF, 0xFF, //5 T
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0x30, 0xFF, 0x20, 0xFF, 0xFF, 0xFF, 0x10, //6 a c g
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0x00, 0xFF, 0xFF, 0xFF, //7 t
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //8
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //9
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //A
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //B
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //C
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //D
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //E
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //F
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF
};
static const uint8_t rv0[256] = {
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //0
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //1
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //2
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //3
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xC0, 0xFF, 0x80, 0xFF, 0xFF, 0xFF, 0x40, //4 A C G
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0x00, 0xFF, 0xFF, 0xFF, //5 T
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xC0, 0xFF, 0x80, 0xFF, 0xFF, 0xFF, 0x40, //6 a c g
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0x00, 0xFF, 0xFF, 0xFF, //7 t
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //8
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //9
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //A
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //B
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //C
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //D
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //E
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //F
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF
};
/*
* For debugging purposes only
*/
const string ReadsProcessor::getBases(const unsigned char* c)
{
string bases = "";
int currentIndex = 0;
int currentOffset = 3;
for (unsigned i = 0; i < m_kmerSize; ++i) {
if (currentOffset == -1) {
currentIndex++;
currentOffset = 3;
}
unsigned char currentChr = c[currentIndex];
currentChr = currentChr >> (2 * currentOffset);
currentChr &= 3;
bases += ("ACGT")[currentChr];
currentOffset--;
}
return bases;
}
/*
* Converts unsigned char * to string given window size specified by this
* object
*/
const string ReadsProcessor::getStr(const unsigned char* c) {
return string(reinterpret_cast<const char*>(c), m_kmerSizeInBytes);
}
/*
* Converts unsigned char * to string given window size specified by this
* object
*/
const string ReadsProcessor::getBinary(const unsigned char* c) {
std::stringstream ss;
for (unsigned i = 0; i < m_kmerSizeInBytes; i++) {
for (unsigned j = 0; j < 8; j++) {
ss << !!((c[i] << j) & 0x80);
}
}
return ss.str();
}
//TODO: find some way of returning position where sequence k-mer is missing
//TODO: NOT THREAD SAFE
/* Prepares DNA sequence for insertion into bloom filter by:
* - Treats lower and upper case the same
* - Also looks into reverse compliment version and returns consistently
* that which is smaller (convention used A<C<G<T, i.e. alphabetical)
* - Returns NULL if k-mer not found
* - m_kmerSize must be greater than 3 otherwise undefined behavior will occur
*/
const unsigned char* ReadsProcessor::prepSeq(string const &sequence,
size_t position)
{
size_t index = position;
size_t revIndex = position + m_kmerSize - 1;
size_t outputIndex = 0;
memset(m_fw, 0, m_kmerSizeInBytes);
memset(m_rv, 0, m_kmerSizeInBytes);
// determines which compliment to use
// parse through string converting and checking for lower-case and non ATCG characters
// half the length of seq because after this point will be palindromic and is not worth checking
for (; outputIndex < m_halfSizeOfKmerInBytes; ++outputIndex) {
//create char for forward
m_fw[outputIndex] |= fw0[static_cast<unsigned char>(sequence[index++])];
m_fw[outputIndex] |= fw1[static_cast<unsigned char>(sequence[index++])];
m_fw[outputIndex] |= fw2[static_cast<unsigned char>(sequence[index++])];
//-128 is used as I am working with signed chars
if (m_fw[outputIndex] == 0xFF
|| fw3[static_cast<unsigned char>(sequence[index])] == 0xFF)
{
return NULL;
}
m_fw[outputIndex] |= fw3[static_cast<unsigned char>(sequence[index++])];
//create char for rv
m_rv[outputIndex] |=
rv0[static_cast<unsigned char>(sequence[revIndex--])];
m_rv[outputIndex] |=
rv1[static_cast<unsigned char>(sequence[revIndex--])];
m_rv[outputIndex] |=
rv2[static_cast<unsigned char>(sequence[revIndex--])];
if (m_rv[outputIndex] == 0xFF
|| rv3[static_cast<unsigned char>(sequence[revIndex])] == 0xFF)
{
return NULL;
}
m_rv[outputIndex] |=
rv3[static_cast<unsigned char>(sequence[revIndex--])];
//compare and convert if not already established
//forward is smaller
if (m_fw[outputIndex] < m_rv[outputIndex]) {
//finish off sequence
for (++outputIndex;
outputIndex + m_hangingBasesExist < m_kmerSizeInBytes;
++outputIndex)
{
//create char for forward
m_fw[outputIndex] |=
fw0[static_cast<unsigned char>(sequence[index++])];
m_fw[outputIndex] |=
fw1[static_cast<unsigned char>(sequence[index++])];
m_fw[outputIndex] |=
fw2[static_cast<unsigned char>(sequence[index++])];
if (m_fw[outputIndex] == 0xFF
|| fw3[static_cast<unsigned char>(sequence[index])]
== 0xFF)
{
return NULL;
}
m_fw[outputIndex] |=
fw3[static_cast<unsigned char>(sequence[index++])];
}
//create last byte
if (m_hangingBasesExist) {
size_t lastPos = position + m_kmerSize - 1;
m_fw[outputIndex] =
fw0[static_cast<unsigned char>(sequence[lastPos--])];
for (; index <= lastPos; --lastPos) {
m_fw[outputIndex] = m_fw[outputIndex] >> 2;
m_fw[outputIndex] |=
fw0[static_cast<unsigned char>(sequence[lastPos])];
}
if (m_fw[outputIndex] == 0xFF) {
return NULL;
}
}
return m_fw;
}
//reverse is smaller
else if (m_fw[outputIndex] > m_rv[outputIndex]) {
//finish off sequence
for (++outputIndex;
outputIndex + m_hangingBasesExist < m_kmerSizeInBytes;
++outputIndex)
{
m_rv[outputIndex] |=
rv0[static_cast<unsigned char>(sequence[revIndex--])];
m_rv[outputIndex] |=
rv1[static_cast<unsigned char>(sequence[revIndex--])];
m_rv[outputIndex] |=
rv2[static_cast<unsigned char>(sequence[revIndex--])];
if (m_rv[outputIndex] == 0xFF
|| rv3[static_cast<unsigned char>(sequence[revIndex])]
== 0xFF)
{
return NULL;
}
m_rv[outputIndex] |=
rv3[static_cast<unsigned char>(sequence[revIndex--])];
}
//create last byte
if (m_hangingBasesExist) {
m_rv[outputIndex] =
rv0[static_cast<unsigned char>(sequence[position++])];
for (; revIndex >= position; ++position) {
m_rv[outputIndex] = m_rv[outputIndex] >> 2;
m_rv[outputIndex] |=
rv0[static_cast<unsigned char>(sequence[position])];
}
if (m_rv[outputIndex] == 0xFF) {
return NULL;
}
}
return m_rv;
}
}
//palamdromic
//finish off sequence
for (++outputIndex; outputIndex + m_hangingBasesExist < m_kmerSizeInBytes;
++outputIndex)
{
//create char for forward
m_fw[outputIndex] |= fw0[static_cast<unsigned char>(sequence[index++])];
m_fw[outputIndex] |= fw1[static_cast<unsigned char>(sequence[index++])];
m_fw[outputIndex] |= fw2[static_cast<unsigned char>(sequence[index++])];
if (m_fw[outputIndex] == 0xFF
|| fw3[static_cast<unsigned char>(sequence[index])] == 0xFF)
{
return NULL;
}
m_fw[outputIndex] |= fw3[static_cast<unsigned char>(sequence[index])];
}
//create last byte
if (m_hangingBases) {
size_t lastPos = position + m_kmerSize - 1;
m_fw[outputIndex] |= fw0[static_cast<unsigned char>(sequence[lastPos])];
for (; index < lastPos; --lastPos) {
m_fw[outputIndex] = m_fw[outputIndex] << 2;
m_fw[outputIndex] |=
fw0[static_cast<unsigned char>(sequence[lastPos])];
}
if (m_fw[outputIndex] == 0xFF) {
return NULL;
}
}
return m_fw;
}
ReadsProcessor::~ReadsProcessor()
{
delete[] m_fw;
delete[] m_rv;
}