/usr/include/blasr/tuples/TupleMatchingImpl.hpp is in libblasr-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.
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 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 | #include <vector>
#include <algorithm>
#include <utility>
#include <iostream>
#include <stdint.h>
#include "Types.h"
#include "NucConversion.hpp"
#include "DNASequence.hpp"
#include "SeqUtils.hpp"
using namespace std;
template<typename Sequence, typename T_TupleList>
int SequenceToTupleList(Sequence &seq, TupleMetrics &tm, T_TupleList &tupleList) {
int s;
typename T_TupleList::Tuple tempTuple;
if (seq.size() < tm.tupleSize) {
return 1;
}
// Otherwise, there is at least one tuple
tupleList.Append(tempTuple);
int res = 0;
for (s = 0; s < seq.length - tm.tupleSize + 1; s++ ) {
if ((res and (res = tempTuple.ShiftAddRL(seq.seq[s+tm.tupleSize-1], tm))) or
(!res and (res = tempTuple.FromStringRL(&seq.seq[s], tm)))) {
tempTuple.ShiftAddRL(seq.seq[s + tm.tupleSize - 1], tm);
tempTuple.pos = s;
tupleList.Append(tempTuple);
}
}
return 1;
}
template<typename TSequence, typename TMatch, typename T_TupleList>
int StoreMatchingPositions(TSequence &querySeq, TupleMetrics &tm, T_TupleList &targetTupleList, vector<TMatch> &matchSet) {
DNALength s;
// TQueryTuple queryTuple;
typename T_TupleList::Tuple queryTuple;
queryTuple.pos = 0;
if (querySeq.length >= tm.tupleSize) {
int res = 0;
for (s = 0; s < querySeq.length - tm.tupleSize + 1; s++) {
if ((res and (res = queryTuple.ShiftAddRL(querySeq.seq[s+tm.tupleSize-1], tm))) or
(!res and (res = queryTuple.FromStringRL(&querySeq.seq[s], tm)))) {
int targetListIndex = 0;
typename vector<typename T_TupleList::Tuple>::const_iterator curIt, endIt;
targetTupleList.FindAll(queryTuple, curIt, endIt);
for(; curIt != endIt; curIt++) {
matchSet.push_back(TMatch(s, (*curIt).pos));
++targetListIndex;
}
}
}
}
return matchSet.size();
}
template<typename Sequence, typename Tuple>
int StoreUniqueTuplePosList(Sequence seq, TupleMetrics &tm, vector<int> &uniqueTuplePosList) {
//
// Do this faster later on with a suffix tree -- faster than n log n construction time.
//
int s;
vector<pair<Tuple, int> > tuples;
Tuple tempTuple;
for (s = 0; s < seq.length - tm.tupleSize + 1; s++) {
tempTuple.FromStringRL(&(seq.seq[s]), tm);
tuples.push_back(make_pair(tempTuple, s));
}
std::sort(tuples.begin(), tuples.end());
int curUnique = 0, curPos = 0;
//
// Filter out the repetitive tuples.
//
while ( curPos < tuples.size() ) {
int nextPos = curPos;
while (nextPos < tuples.size() and tuples[nextPos] == tuples[curPos])
nextPos++;
if (nextPos - curPos == 1) {
tuples[curUnique].first == tuples[curPos].first;
uniqueTuplePosList.push_back(tuples[curUnique].second);
++curUnique;
++curPos;
}
else {
curPos = nextPos;
}
}
//
// Be nice and leave the pos list in ascending sorted order,
// even though the top of this function does not specify it.
//
std::sort(uniqueTuplePosList.begin(), uniqueTuplePosList.end());
return uniqueTuplePosList.size();
}
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