/usr/include/pbseq/pbdata/PackedDNASequence.hpp is in libpbdata-dev 0~20161219-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 | #ifndef _BLASR_PACKED_DNA_SEQUENCE_HPP_
#define _BLASR_PACKED_DNA_SEQUENCE_HPP_
#include <fstream>
#include "DNASequence.hpp"
#include "NucConversion.hpp"
#include "utils/BitUtils.hpp"
/*
* Implement a structure to maintain DNA as 3 bits per nucleotide.
* The extra bit is required for N's in the sequence. A key is that
* this structure is read-only through the operator[]. It may be set
* with the PackedDNASequence::Set(pos,value) command.
*/
typedef unsigned int PackedDNAWord;
class PackedDNASequence {
public:
static const PackedDNAWord Mask2All = 613566756; //100100100...
static const PackedDNAWord Mask1All = 306783378; //010010010...
static const PackedDNAWord Mask0All = 153391689; //001001001...
static const PackedDNAWord xorMask[];
static const PackedDNAWord NucPosMask[];
static const PackedDNAWord NegMask[];
static const PackedDNAWord MaskRL[];
static const PackedDNAWord MaskLR[];
static const PackedDNAWord NucMask = 7;
static const DNALength NucsPerWord = 10;
PackedDNAWord *seq;
int nCountInWord;
int nCountNuc;
DNALength length;
DNALength arrayLength;
Nucleotide Get(DNALength pos);
Nucleotide operator[](DNALength pos);
PackedDNASequence();
~PackedDNASequence();
void Allocate(DNALength numberOfNucleotides);
void CreateFromDNASequence(DNASequence &dnaSeq);
void Set(DNALength pos, Nucleotide threeBitValue);
DNALength CountInWord(PackedDNAWord word, PackedDNAWord wordMask, Nucleotide nuc);
DNALength CountNuc(DNALength start, DNALength end, Nucleotide nuc);
void Write(std::ostream &out);
void Read(std::istream &in);
void PrintUnpacked(std::ostream &out, int lineLength = 50);
};
#endif // _BLASR_PACKED_DNA_SEQUENCE_HPP_
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