void wigTestMaker(char *outDir)
/* wigTestMaker - Create test wig files.. */
{
makeDir(outDir);
setCurrentDir(outDir);
makeChromSizes("chrom.sizes", 100);
makeEmpty("empty.wig");
makeEmptyFixed("emptyFixed.wig");
makeEmptyVar("emptyVar.wig");
makeShortFixed("shortFixed.wig");
makeShortVar("shortVar.wig");
makeShortBed("shortBed.wig");
makeSineSineFixed("sineSineFixed.wig", 1000, 500, 10, 8);
makeSineSineVar("sineSineVar.wig", 1000, 500, 10, 4);
makeSineSineBed("sineSineBed.wig", 1000, 500, 10, 2);
makeIncreasing("increasing.wig");
makeMixem("mixem.wig");
makeContigSizes("contig.sizes", 666666);
makeManyContigs("contigs.wig", 666666);
}
//[[Rcpp::export]]
DataFrame flank_impl(DataFrame inputTable, DataFrame genome,
double both = 0, double left = 0, double right = 0,
bool fraction = false, bool strand = false, bool trim = false) {
// Warnings
if (both == 0 & left == 0 & right == 0)
stop("specify one of both, left, right");
if (both != 0 & (left != 0 || right != 0))
stop("ambiguous side spec for bed_flank");
std::vector<std::string> TableNames = inputTable.names();
int TableLen = TableNames.size();
bool strandTest = false;
for (int i = 0; i < TableLen; i++)
if (TableNames[i] == "strand")
strandTest = true;
if (strand == true & strandTest == false)
stop("expected strand column");
// Set both
if (both > 0) left = right = both;
// Set input and output vectors
std::vector<std::string> chroms = inputTable["chrom"];
std::vector<int> startCoords = inputTable["start"];
std::vector<int> endCoords = inputTable["end"];
int N = startCoords.size();
std::vector<int> coordSize(N);
std::vector<int> idxOut;
std::vector<double> startOut;
std::vector<double> endOut;
// Create unordered map for chrom sizes
genome_map_t chroMap = makeChromSizes(genome);
for (int i = 0; i < N; i++) {
int leftstart;
int leftend;
int rightstart;
int rightend;
// strand
if (strand == true) {
std::vector<std::string> strands = inputTable["strand"];
// strand, fraction
if (fraction == true) {
coordSize[i] = endCoords[i] - startCoords[i];
if (strands[i] == "+") {
leftstart = startCoords[i] - coordSize[i] * left;
leftend = startCoords[i];
rightstart = endCoords[i];
rightend = endCoords[i] + coordSize[i] * right;
} else {
leftstart = endCoords[i];
leftend = endCoords[i] + coordSize[i] * left;
rightstart = startCoords[i] - coordSize[i] * right;
rightend = startCoords[i];
}
// strand, no fraction
} else {
if (strands[i] == "+") {
leftstart = startCoords[i] - left;
leftend = startCoords[i];
rightstart = endCoords[i];
rightend = endCoords[i] + right;
} else {
leftstart = endCoords[i];
leftend = endCoords[i] + left;
rightstart = startCoords[i] - right;
rightend = startCoords[i];
}
}
// no strand
} else {
// no strand, fraction
if (fraction == true) {
coordSize[i] = endCoords[i] - startCoords[i];
leftstart = startCoords[i] - coordSize[i] * left;
leftend = startCoords[i];
rightstart = endCoords[i];
rightend = endCoords[i] + coordSize[i] * right;
// no strand, no fraction
} else {
leftstart = startCoords[i] - left;
leftend = startCoords[i];
rightstart = endCoords[i];
rightend = endCoords[i] + right;
}
}
// Compare new intervals to chrom sizes
std::string chrom = chroms[i];
int chrSize = chroMap[chrom];
if (left > 0 & leftstart > 0 & leftend <= chrSize) {
startOut.push_back (leftstart);
endOut.push_back (leftend);
idxOut.push_back (i);
} else if (trim == true & leftstart > 0 & leftend > chrSize) {
startOut.push_back (leftstart);
endOut.push_back (chrSize);
idxOut.push_back (i);
} else if (trim == true & leftstart <= 0 & leftend <= chrSize) {
startOut.push_back (1);
endOut.push_back (leftend);
idxOut.push_back (i);
} else if (trim == true & leftstart <= 0 & leftend > chrSize) {
startOut.push_back (1);
endOut.push_back (chrSize);
idxOut.push_back (i);
}
if (right > 0 & rightstart > 0 & rightend <= chrSize) {
startOut.push_back (rightstart);
endOut.push_back (rightend);
idxOut.push_back (i);
} else if (trim == true & rightstart > 0 & rightend > chrSize) {
startOut.push_back (rightstart);
endOut.push_back (chrSize);
idxOut.push_back (i);
} else if (trim == true & rightstart <= 0 & rightend <= chrSize) {
startOut.push_back (1);
endOut.push_back (rightend);
idxOut.push_back (i);
} else if (trim == true & rightstart <= 0 & rightend > chrSize) {
startOut.push_back (1);
endOut.push_back (chrSize);
idxOut.push_back (i);
}
}
// Write new DataFrame
DataFrame outTable = DataFrameSubsetVisitors(inputTable, names(inputTable)).subset(idxOut, "data.frame");
outTable["start"] = startOut;
outTable["end"] = endOut;
return outTable;
}
//[[Rcpp::export]]
DataFrame complement_impl(GroupedDataFrame gdf, DataFrame genome) {
genome_map_t chrom_sizes = makeChromSizes(genome) ;
DataFrame df = gdf.data() ;
IntegerVector starts = df["start"] ;
IntegerVector ends = df["end"] ;
CharacterVector chroms = df["chrom"] ;
std::vector<std::string> chroms_out ;
std::vector<int> starts_out ;
std::vector<int> ends_out ;
int ngroups = gdf.ngroups() ;
GroupedDataFrame::group_iterator git = gdf.group_begin() ;
for (int i = 0; i < ngroups; ++i, ++git) {
SlicingIndex indices = *git ;
int ni = indices.size() ;
int start, end ;
int last_end = 1 ;
// get chrom from first index
auto chrom = as<std::string>(chroms[indices[0]]) ;
for (int j = 0; j < ni; ++j) {
start = starts[indices[j]] ;
end = ends[indices[j]] ;
if (j == 0) {
if (start == 1) {
last_end = end ;
continue ;
} else {
chroms_out.push_back(chrom) ;
starts_out.push_back(1) ;
ends_out.push_back(start) ;
}
} else {
chroms_out.push_back(chrom) ;
starts_out.push_back(last_end) ;
ends_out.push_back(start) ;
}
last_end = end;
}
auto chrom_size = chrom_sizes[chrom] ;
if (last_end < chrom_size) {
chroms_out.push_back(chrom) ;
starts_out.push_back(last_end) ;
ends_out.push_back(chrom_size) ;
}
}
return DataFrame::create(_("chrom") = chroms_out,
_("start") = starts_out,
_("end") = ends_out,
_("stringsAsFactors") = false) ;
}
