bool ContextBase::determineOutputType() {
if (_outputTypeDetermined) {
return true;
}
//test whether output should be BED or BAM.
//If the user explicitly requested BED, then it's BED.
if (getExplicitBedOutput()) {
setOutputFileType(FileRecordTypeChecker::SINGLE_LINE_DELIM_TEXT_FILE_TYPE);
_outputTypeDetermined = true;
return true;
}
//Otherwise, if the input is BAM, then the output is BAM
int fileIdx = hasIntersectMethods() ? _queryFileIdx : 0;
if (_files[fileIdx]->getFileType() == FileRecordTypeChecker::BAM_FILE_TYPE) {
setOutputFileType(FileRecordTypeChecker::BAM_FILE_TYPE);
return true;
}
//Okay, it's bed.
setOutputFileType(FileRecordTypeChecker::SINGLE_LINE_DELIM_TEXT_FILE_TYPE);
_outputTypeDetermined = true;
return true;
}
bool ContextBase::isValidState()
{
if (!openFiles()) {
return false;
}
if (!cmdArgsValid()) {
return false;
}
if (!determineOutputType()) {
return false;
}
if (_program != GROUP_BY &&
_files[0]->getRecordType() == FileRecordTypeChecker::NO_POS_PLUS_RECORD_TYPE)
{
_errorMsg = "ERROR: file ";
_errorMsg.append(_files[0]->getFileName());
_errorMsg.append(" has non positional records, which are only valid for \n");
_errorMsg.append(" the groupBy tool. Perhaps you are using a header");
_errorMsg.append(" line(s) that starts with \n");
_errorMsg.append(" something other than \"#\", \"chrom\", or \"chr\" (any case)?");
return false;
}
if (getObeySplits()) {
_splitBlockInfo = new BlockMgr(_overlapFractionA, _reciprocalFraction);
}
if (hasColumnOpsMethods()) {
if (hasIntersectMethods()) {
for (int i=0; i < (int)_dbFileIdxs.size(); i++) {
FileRecordMgr *dbFile = getFile(_dbFileIdxs[i]);
_keyListOps->setDBfileType(dbFile->getFileType());
if (!_keyListOps->isValidColumnOps(dbFile)) {
return false;
}
}
} else {
FileRecordMgr *dbFile = getFile(0);
_keyListOps->setDBfileType(dbFile->getFileType());
if (!_keyListOps->isValidColumnOps(dbFile)) {
return false;
}
}
//if user specified a precision, pass it to
//keyList ops
if (_reportPrecision != -1) {
_keyListOps->setPrecision(_reportPrecision);
}
}
return true;
}
int ContextBase::getBamHeaderAndRefIdx() {
if (_bamHeaderAndRefIdx != -1) {
//already found which BAM file to use for the header
return _bamHeaderAndRefIdx;
}
if (hasIntersectMethods()) {
if (_files[_queryFileIdx]->getFileType() == FileRecordTypeChecker::BAM_FILE_TYPE) {
_bamHeaderAndRefIdx = _queryFileIdx;
} else {
_bamHeaderAndRefIdx = _dbFileIdxs[0];
}
return _bamHeaderAndRefIdx;
}
if (_files[0]->getFileType() == FileRecordTypeChecker::BAM_FILE_TYPE) {
_bamHeaderAndRefIdx = 0;
return _bamHeaderAndRefIdx;
}
return _bamHeaderAndRefIdx;
}
bool ContextBase::isValidState()
{
if (!openFiles()) {
return false;
}
if (!cmdArgsValid()) {
return false;
}
if (!determineOutputType()) {
return false;
}
if (hasColumnOpsMethods()) {
FileRecordMgr *dbFile = getFile(hasIntersectMethods() ? _databaseFileIdx : 0);
_keyListOps->setDBfileType(dbFile->getFileType());
if (!_keyListOps->isValidColumnOps(dbFile)) {
return false;
}
}
return true;
}
bool ContextBase::isValidState()
{
if (!openFiles()) {
return false;
}
if (!cmdArgsValid()) {
return false;
}
if (!determineOutputType()) {
return false;
}
if (getObeySplits()) {
_splitBlockInfo = new BlockMgr(_overlapFraction, _reciprocal);
}
if (hasColumnOpsMethods()) {
if (hasIntersectMethods()) {
for (int i=0; i < (int)_dbFileIdxs.size(); i++) {
FileRecordMgr *dbFile = getFile(_dbFileIdxs[i]);
_keyListOps->setDBfileType(dbFile->getFileType());
if (!_keyListOps->isValidColumnOps(dbFile)) {
return false;
}
}
} else {
FileRecordMgr *dbFile = getFile(0);
_keyListOps->setDBfileType(dbFile->getFileType());
if (!_keyListOps->isValidColumnOps(dbFile)) {
return false;
}
}
//if user specified a precision, pass it to
//keyList ops
if (_reportPrecision != -1) {
_keyListOps->setPrecision(_reportPrecision);
}
}
return true;
}