// build
BedCoverage::BedCoverage(string &bedAFile, string &bedBFile, bool forceStrand,
bool writeHistogram, bool bamInput, bool obeySplits, bool eachBase) {
_bedAFile = bedAFile;
_bedBFile = bedBFile;
_bedA = new BedFile(bedAFile);
_bedB = new BedFile(bedBFile);
_forceStrand = forceStrand;
_obeySplits = obeySplits;
_eachBase = eachBase;
_writeHistogram = writeHistogram;
_bamInput = bamInput;
if (_bamInput == false)
CollectCoverageBed();
else
CollectCoverageBam(_bedA->bedFile);
}
// build
BedCoverage::BedCoverage(string &bedAFile, string &bedBFile, bool sameStrand, bool diffStrand,
bool writeHistogram, bool bamInput, bool obeySplits,
bool eachBase, bool countsOnly) {
_bedAFile = bedAFile;
_bedBFile = bedBFile;
_bedA = new BedFile(bedAFile);
_bedB = new BedFile(bedBFile);
_sameStrand = sameStrand;
_diffStrand = diffStrand;
_obeySplits = obeySplits;
_eachBase = eachBase;
_writeHistogram = writeHistogram;
_bamInput = bamInput;
_countsOnly = countsOnly;
if (_bamInput == false)
CollectCoverageBed();
else
CollectCoverageBam(_bedA->bedFile);
}