int main(int argc, char* argv[]) {
if (argc < 3) {
cout << "usage: samatcher queryfile targetfile" <<endl;
exit(1);
}
string queryFileName, targetFileName;
int minMatchLength = 5;
int maxExpand = 0;
queryFileName = argv[1];
targetFileName = argv[2];
int argi = 3;
AnchorParameters anchorParams;
while (argi < argc) {
if (strcmp(argv[argi], "-minmatch") == 0) {
anchorParams.minMatchLength = atoi(argv[++argi]);
}
else if (strcmp(argv[argi], "-maxexpand") == 0) {
anchorParams.expand = atoi(argv[++argi]);
}
else {
cout << "ERROR! Invalid argument: " << argv[argi]<< endl;
exit(1);
}
++argi;
}
FASTQSequence query, target;
FASTAReader queryReader, targetReader;
queryReader.Init(queryFileName);
targetReader.Init(targetFileName);
while(1) {
if (!queryReader.GetNext(query)) break;
if (!targetReader.GetNext(target)) break;
query.ToUpper();
target.ToUpper();
//
// Build the suffix array on the target.
//
DNASuffixArray sarray;
target.ToThreeBit();
vector<int> alphabet;
sarray.InitThreeBitDNAAlphabet(alphabet);
sarray.LarssonBuildSuffixArray(target.seq, target.length, alphabet);
cout <<"done building suffix array." << endl;
target.ToAscii();
//
// Find the list of anchors.
//
query.PrintSeq(cout);
cout << "target: " << endl;
target.PrintSeq(cout);
MatchPosList matchPosList;
int numKeysMatched;
anchorParams.useLookupTable = false;
numKeysMatched =
MapReadToGenome(target, sarray, query, sarray.lookupPrefixLength,
matchPosList, anchorParams);
//
// Now, convert the matchPosList to a set of fragments
// that can be used in the sdp.
//
SortMatchPosList(matchPosList);
vector<ChainedFragment> fragments;
fragments.resize(matchPosList.size());
VectorIndex i;
for (i = 0; i < matchPosList.size(); i++) {
fragments[i].x = matchPosList[i].t;
fragments[i].y = matchPosList[i].q;
fragments[i].length = fragments[i].weight = matchPosList[i].w;
// cout << fragments[i].x << " " << fragments[i].y << " " << fragments[i].weight << endl;
}
cout << "stored a total of: " << fragments.size() << " fragments." << endl;
int maxFragmentChainLength;
vector<DNALength> maxFragmentChain;
maxFragmentChainLength = GlobalChain<ChainedFragment, BasicEndpoint<ChainedFragment> >(fragments, maxFragmentChain);
MatchedAlignment alignment;
std::reverse(maxFragmentChain.begin(), maxFragmentChain.end());
alignment.AllocateBlocks(maxFragmentChain.size());
for (i = 0; i < maxFragmentChain.size(); i++) {
alignment.blocks[i].qPos = fragments[maxFragmentChain[i]].y;
alignment.blocks[i].tPos = fragments[maxFragmentChain[i]].x;
alignment.blocks[i].length = fragments[maxFragmentChain[i]].length;
cout << "( " << fragments[maxFragmentChain[i]].x << " "
<< fragments[maxFragmentChain[i]].y << " "
<< fragments[maxFragmentChain[i]].length << ") ";
}
cout << endl;
alignment.tStart = alignment.qStart = 0;
alignment.tPos = alignment.qPos = 0;
StickPrintAlignment(alignment, query, target, cout);
}
return 0;
}
void StoreNonOverlappingIndices(std::vector<T_MatchPos> &lis,
std::vector<T_MatchPos> &noOvpLis) {
unsigned int i;
//
// Greedily add lis matches according to weight. A match may be added
// as long as it does not overlap with any other matches.
//
// do nothing on empty lists
if (lis.empty()) return;
//
// First build a list of matches sorted by weight.
SortMatchPosListByWeight(lis);
//
// The first match is guaranteed to not overlap.
noOvpLis.push_back(lis[0]);
//
// Nothing is overlapping, and everything is sorted when there is
// just one value.
if (lis.size() == 1) return;
//
// Next, add matches as long as they do not overlap.
for (i = 1; i < lis.size(); i++ ){
VectorIndex j;
int lts = lis[i].t;
int lte = lis[i].t + lis[i].GetLength();
int lqs = lis[i].q;
int lqe = lis[i].q + lis[i].GetLength();
int ovpFound = 0;
for (j =0; j < noOvpLis.size(); j++ ){
int tIntvStart = noOvpLis[j].t;
int tIntvEnd = noOvpLis[j].t + noOvpLis[j].GetLength();
int qIntvStart = noOvpLis[j].q;
int qIntvEnd = noOvpLis[j].q + noOvpLis[j].GetLength();
if ((lts >= tIntvStart and lts < tIntvEnd) or
(lte > tIntvStart and lte <= tIntvEnd) or
(lqs >= qIntvStart and lqs < qIntvEnd) or
(lqe > qIntvStart and lqe <= qIntvEnd)) {
ovpFound = 1;
break;
}
}
if (!ovpFound) {
noOvpLis.push_back(lis[i]);
}
}
//
// Now, the matches are found in order of size, but they need to
// be stored in order of text.
//
SortMatchPosList(noOvpLis);
//
// The match pos list was sorted in order of weight.
// Just in case it causes problems down the line, re-sort it
// according to query pos.
//
lis = noOvpLis;
SortMatchPosList(lis);
}
