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#ifndef _BLASR_COMPRESSED_DNA_SEQUENCE_HPP_
#define _BLASR_COMPRESSED_DNA_SEQUENCE_HPP_
#include <cstring>
#include <pbdata/defs.h>
#include <pbdata/Compare4BitCompressed.hpp>
#include <pbdata/DNASequence.hpp>
#include <pbdata/FASTASequence.hpp>
#include <pbdata/qvs/QualityValue.hpp>
typedef unsigned char CompressedNucleotide;
class CompressedDNASequence : public DNASequence
{
static const unsigned char MaskCount = 0xf;
static const unsigned char MaskNuc = 0xf0;
static const unsigned char ShiftCount = 4;
public:
char *title;
int titleLength;
//
// This is just a placeholder for now.
// No extra data here, just the ability to decompress. Right now
// the utilities for the compressed dna sequences
// are in CompressedSeqUtils.h, which could move here later.
//
QualityValue *qual;
CompressedDNASequence()
{
const char t[] = "Compressed sequence\0";
titleLength = strlen(t);
title = ProtectedNew<char>(titleLength + 1);
strcpy(title, t);
title[titleLength] = '\0';
}
void MakeRC(CompressedDNASequence &rc)
{
rc.Allocate(length);
DNALength i;
for (i = 0; i < length; i++) {
rc.seq[length - i - 1] = ReverseComplementNuc[ThreeBit[seq[i] & MaskCount]];
rc.seq[length - i - 1] += (seq[i] & MaskNuc);
}
memcpy(rc.title, title, titleLength);
rc.titleLength = titleLength;
}
Nucleotide operator[](DNALength i) { return GetNuc(i); }
Nucleotide GetNuc(DNALength i) { return (seq[i] & MaskCount); }
unsigned char GetCount(DNALength i) { return seq[i] >> ShiftCount; }
char *GetName() { return (char *)title; }
void Copy(FASTASequence &rhs)
{
seq = ProtectedNew<CompressedNucleotide>(rhs.length);
memcpy(seq, rhs.seq, rhs.length);
length = rhs.length;
if (title != NULL) {
delete[] title;
}
title = ProtectedNew<char>(rhs.titleLength + 1);
memcpy(title, rhs.title, rhs.titleLength);
titleLength = rhs.titleLength;
title[titleLength] = '\0';
}
float GetAverageQuality() { return 0.0; }
void SortHomopolymerQualities()
{
std::cout << "qualities are not implemented for compressed sequences." << std::endl;
assert(0);
}
};
#endif
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