/usr/include/pbdata/CompressedSequenceImpl.hpp is in libpbdata-dev 0~20151014+gitbe5d1bf-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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#define _BLASR_COMPRESSED_SEQUENCES_IMPL_HPP_
#include "utils.hpp"
template<typename T_Sequence>
void CompressedSequence<T_Sequence>::CopyConfiguration(CompressedSequence<T_Sequence> &rhs) {
hasIndex = rhs.hasIndex;
hasTitle = rhs.hasTitle;
}
template<typename T_Sequence>
void CompressedSequence<T_Sequence>::ShallowCopy(CompressedSequence<T_Sequence> &rhs) {
//
// Copy over non sequence information
index.ShallowCopy(rhs.index);
CopyConfiguration(rhs);
// Copy sequence information
((FASTASequence*)this)->ShallowCopy((FASTASequence&)rhs);
}
template<typename T_Sequence>
void CompressedSequence<T_Sequence>::MakeRC(CompressedSequence &rc) {
rc.Free(); //Free rc.seq and rc.title before allocate.
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);
}
rc.CopyTitle(title, titleLength);
}
template<typename T_Sequence>
Nucleotide CompressedSequence<T_Sequence>::operator[](DNALength i) {
return GetNuc(i);
}
template<typename T_Sequence>
Nucleotide CompressedSequence<T_Sequence>::GetNuc(DNALength i) {
return (seq[i] & MaskCount);
}
template<typename T_Sequence>
unsigned char CompressedSequence<T_Sequence>::GetCount(DNALength i) {
return seq[i] >> ShiftCount;
}
template<typename T_Sequence>
char* CompressedSequence<T_Sequence>::GetName() {
return (char*) title;
}
template<typename T_Sequence>
void CompressedSequence<T_Sequence>::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';
}
template<typename T_Sequence>
float CompressedSequence<T_Sequence>::GetAverageQuality() {
return 0.0;
}
template<typename T_Sequence>
void CompressedSequence<T_Sequence>::SortHomopolymerQualities() {
std::cout << "qualities are not implemented for compressed sequences."
<< std::endl;
}
template<typename T_Sequence>
CompressedSequence<T_Sequence>::CompressedSequence() {
hasIndex = 0;
hasTitle = 0;
qual = NULL;
FASTASequence();
}
template<typename T_Sequence>
CompressedSequence<T_Sequence>::~CompressedSequence() {
CompressedSequence::Free();
}
template<typename T_Sequence>
void CompressedSequence<T_Sequence>::Free() {
if (hasIndex) {
index.Free();
}
if(qual) {delete [] qual; qual = NULL;}
FASTASequence::Free();
hasIndex = 0;
hasTitle = 0;
}
template<typename T_Sequence>
void CompressedSequence<T_Sequence>::SetHasTitle() {
hasTitle = 1;
}
template<typename T_Sequence>
void CompressedSequence<T_Sequence>::SetHasIndex() {
hasIndex = 1;
}
template<typename T_Sequence>
void CompressedSequence<T_Sequence>::Write(std::string outFileName) {
std::ofstream out;
CrucialOpen(outFileName,out, std::ios::binary | std::ios::in);
out.write((char*) &hasTitle, sizeof(int));
out.write((char*) &hasIndex, sizeof(int));
if (hasTitle) {
out.write((char*)&titleLength, sizeof(int));
out.write((char*)title, titleLength);
}
out.write((char*) &length, sizeof(int));
out.write((char*) seq, sizeof(char) * length);
if (hasIndex) {
index.Write(out);
}
out.close();
}
template<typename T_Sequence>
void CompressedSequence<T_Sequence>::Read(std::string inFileName) {
Free(); //Free before reusing this object.
std::ifstream in;
CrucialOpen(inFileName, in, std::ios::binary | std::ios::in);
// step 1, read in the options.
in.read((char*) &hasTitle, sizeof(int));
in.read((char*) &hasIndex, sizeof(int));
if (hasTitle) {
int inTitleLength;
in.read((char*) &inTitleLength, sizeof(int));
char * inTitle = ProtectedNew<char>(inTitleLength+1);
in.read((char*) inTitle, inTitleLength);
inTitle[titleLength] = '\0';
CopyTitle(inTitle, inTitleLength);
delete [] inTitle;
}
in.read((char*) &length, sizeof(DNALength));
seq = ProtectedNew<Nucleotide>(length);
in.read((char*) seq, length * sizeof(Nucleotide));
if (hasIndex) {
index.Read(in);
}
deleteOnExit = true;
}
template<typename T_Sequence>
int CompressedSequence<T_Sequence>::BuildFourBitReverseIndex(int binSize) {
BuildReverseIndex(15, binSize);
}
template<typename T_Sequence>
int CompressedSequence<T_Sequence>::BuildReverseIndex(int maxRun, int binSize) {
hasIndex = 1;
DNALength i;
DNALength hpi;
//
// Phase 1. Count the number of nucleotide transitions-1
//
hpi = 0;
for (i = 0; i < length; i++) {
// if (hpi % binSize == 0 ){
// index.push_back(i);
// }
int run = 1;
while (i < length - 1
and ThreeBit[seq[i]] == ThreeBit[seq[i+1]] and
(run == 0 or
run < maxRun)) {i++, run++;};
hpi++;
}
//
// Phase 2. Store the index.
//
index.Free();
index.indexLength = hpi/index.binSize + 1;
index.index = ProtectedNew<int>(index.indexLength);
hpi = 0;
int ii = 0;
for (i = 0; i < length; i++) {
if (hpi % index.binSize == 0 ) {
assert(ii < index.indexLength);
index.index[ii] = i;
++ii;
}
int run = 1;
while (i < length - 1
and ThreeBit[seq[i]] == ThreeBit[seq[i+1]] and
(run == 0 or
run < maxRun)) {i++, run++;};
hpi++;
}
return index.size();
}
template<typename T_Sequence>
long CompressedSequence<T_Sequence>::Lookup4BitCompressedSequencePos(int cpPos) {
int bin = cpPos / index.binSize;
int origPos = index.index[bin];
int cpBinPos = bin * index.binSize;
int cp;
for (cp = cpBinPos; cp < cpPos; cp++ ){
origPos += GetCount(seq[cp]);
}
return origPos;
}
template<typename T_Sequence>
int CompressedSequence<T_Sequence>::LookupSequencePos(int hpPos) {
int origPos = index.index[hpPos % index.binSize];
int hpi;
for (hpi = (hpPos / index.binSize) * index.binSize; hpi < hpPos; hpi++, origPos++ ) {
//
// advance orig across all homopolymer stretches.
//
while (origPos < length - 1 and
seq[origPos] == seq[origPos+1])
++origPos;
}
return origPos;
}
template<typename T_Sequence>
char CompressedSequence<T_Sequence>::GetCount(unsigned char ch) {
return (ch >> 4);
}
template<typename T_Sequence>
DNALength CompressedSequence<T_Sequence>::FourBitCompressHomopolymers() {
VectorIndex i, c;
unsigned char count = 0;
for (i =0, c = 0; i < length; c++, i++) {
count = 1;
while (count < 15 and
i < length - 1
and ThreeBit[seq[i]] == ThreeBit[seq[i+1]]) {
i++; count++;
}
// store nuc into the lower 4 bits
seq[c] = ThreeBit[seq[i]];
// store count into the upper 4 bits.
count = count << 4;
seq[c] = seq[c] | count;
}
length = c;
return length;
}
template<typename T_Sequence>
int CompressedSequence<T_Sequence>::Only4BitACTG(CompressedNucleotide *seq, int seqLength) {
int i;
for (i = 0; i < seqLength; i++ ){
if (ThreeBit[seq[i] & MaskCount] > 3) {
return 0;
}
}
return 1;
}
template<typename T_Sequence>
int CompressedSequence<T_Sequence>::Only4BitACTG() {
return Only4BitACTG(seq, length);
}
template<typename T_Sequence>
void CompressedSequence<T_Sequence>::RemoveCompressionCounts() {
DNALength i;
unsigned char mask =0xf;
for (i = 0; i< length; i++) {
seq[i] = seq[i] & mask;
}
}
template<typename T_Sequence>
DNALength CompressedSequence<T_Sequence>::FourBitDecompressHomopolymers(int start, int end,
T_Sequence &decompSeq) {
decompSeq.Free(); // Free before decomp;
//
// first compute the length of the decoded
//
DNALength i;
decompSeq.length = 0;
for (i = start; i < end; i++ ){
unsigned char count;
count = (unsigned char) seq[i];
count >>= 4;
decompSeq.length += count;
}
decompSeq.seq = ProtectedNew<Nucleotide>(decompSeq.length);
//
// Now store the actual decompressed seq.
//
int d = 0;
unsigned char mask = 0xf;
for (i = start; i < end; i++ ){
unsigned char count;
count = (unsigned char) seq[i];
count >>= 4;
int j;
for (j = 0; j < count; j++ ){
decompSeq.seq[d] = FourBitToAscii[(seq[i] & mask)];
d++;
}
}
decompSeq.bitsPerNuc = 4;
decompSeq.deleteOnExit = true;
return decompSeq.length;
}
template<typename T_Sequence>
DNALength CompressedSequence<T_Sequence>::CondenseHomopolymers() {
VectorIndex i, c;
for (i =0, c = 0; i < length; c++, i++) {
while (i < length - 1 and ThreeBit[seq[i]] == ThreeBit[seq[i+1]]) i++;
seq[c] = seq[i];
}
length = c;
return length;
}
#endif
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