bool ContextBase::openFiles() { //Make a vector of FileRecordMgr objects by going through the vector //of filenames and opening each one. if (_allFilesOpened) { return true; } if (_fileNames.size() == 0) { //No input was specified. Error and exit. _errorMsg += "\n***** ERROR: No input file given. Exiting. *****"; return false; } _files.resize(_fileNames.size()); for (int i = 0; i < (int)_fileNames.size(); i++) { FileRecordMgr *frm = getNewFRM(_fileNames[i], i); if (hasGenomeFile()) { frm->setGenomeFile(_genomeFile); } //If we're going to do column operations, and an input file // is BAM, we'll need the full flags. if (hasColumnOpsMethods()) { setUseFullBamTags(true); } frm->setFullBamFlags(_useFullBamTags); frm->setIsSorted(_sortedInput); frm->setIoBufSize(_ioBufSize); frm->setIsGroupBy(_program == GROUP_BY); if (!frm->open(_inheader)) { return false; } if (_noEnforceCoordSort) { frm->setNoEnforceCoodSort(true); } _files[i] = frm; } _allFilesOpened = true; return true; }
bool ContextBase::openFiles() { //Make a vector of FileRecordMgr objects by going through the vector //of filenames and opening each one. if (_allFilesOpened) { return true; } _files.resize(_fileNames.size()); for (int i = 0; i < (int)_fileNames.size(); i++) { FileRecordMgr *frm = new FileRecordMgr(_fileNames[i], _sortedInput); if (hasGenomeFile()) { frm->setGenomeFile(_genomeFile); } frm->setFullBamFlags(_useFullBamTags); if (!frm->open()) { return false; } _files[i] = frm; } _allFilesOpened = true; return true; }