// 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); }