/usr/include/pbseq/pbdata/CompressedDNASequence.hpp is in libpbdata-dev 0~20161219-2.
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 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 | #ifndef _BLASR_COMPRESSED_DNA_SEQUENCE_HPP_
#define _BLASR_COMPRESSED_DNA_SEQUENCE_HPP_
#include "DNASequence.hpp"
#include "FASTASequence.hpp"
#include "defs.h"
#include <string.h>
#include "qvs/QualityValue.hpp"
#include "Compare4BitCompressed.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() {
cout << "qualities are not implemented for compressed sequences." << endl;
assert(0);
}
};
#endif
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