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
if (getFile(0)->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::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 there are any BAM files in the input,
//then the output should be BAM.
for (_i = 0; _i < (int)_files.size(); _i++) {
if (_files[_i]->getFileType() == FileRecordTypeChecker::BAM_FILE_TYPE) {
setOutputFileType(FileRecordTypeChecker::BAM_FILE_TYPE);
_bamHeaderAndRefIdx = _i;
_outputTypeDetermined = true;
return true;
}
}
//Okay, it's bed.
setOutputFileType(FileRecordTypeChecker::SINGLE_LINE_DELIM_TEXT_FILE_TYPE);
_outputTypeDetermined = true;
return true;
}
bool ContextIntersect::determineOutputType() {
if (_outputTypeDetermined) {
return true;
}
//determine the maximum number of database fields.
for (int i=0; i < getNumDatabaseFiles(); i++) {
int numFields = getDatabaseFile(i)->getNumFields();
if ( numFields > _maxNumDatabaseFields) {
_maxNumDatabaseFields = numFields;
}
}
//If the query is BAM, and bed output wasn't specified, then the output is BAM.
if (getQueryFileType() == FileRecordTypeChecker::BAM_FILE_TYPE && !getExplicitBedOutput()) {
setOutputFileType(FileRecordTypeChecker::BAM_FILE_TYPE);
_outputTypeDetermined = true;
return true;
}
return ContextBase::determineOutputType();
}
bool ContextIntersect::isValidState()
{
if (!ContextBase::isValidState()) {
return false;
}
if (_queryFileIdx == -1 || _dbFileIdxs.size() == -0) {
_errorMsg = "\n***** ERROR: query and database files not specified. *****";
return false;
}
if (getAnyHit() && getNoHit()) {
_errorMsg = "\n***** ERROR: request either -u for anyHit OR -v for noHit, not both. *****";
return false;
}
if (getWriteCount()) {
if (getAnyHit()) {
_errorMsg = "\n***** ERROR: request either -c for writeCount OR -u for anyHit, not both. *****";
return false;
} else if (getWriteB()) {
_errorMsg = "\n***** ERROR: request either -c for writeCount OR -wb for writeB, not both. *****";
return false;
} else if (getQueryFileType() == FileRecordTypeChecker::BAM_FILE_TYPE && !getExplicitBedOutput()) {
_errorMsg = "\n***** ERROR: writeCount option is not valid with BAM query input, unless bed output is specified with -bed option. *****";
return false;
}
}
if (_haveFraction && (_overlapFraction <= 0.0 || _overlapFraction > 1.0)) {
_errorMsg = "\n***** ERROR: _overlapFraction must be in the range (0.0, 1.0]. *****";
return false;
}
if (getUseDBnameTags() && _dbNameTags.size() != _dbFileIdxs.size()) {
_errorMsg = "\n***** ERROR: Number of database name tags given does not match number of databases. *****";
return false;
}
if (getWriteOverlap()) {
if (getWriteA()) {
_errorMsg = "\n***** ERROR: request either -wa for writeA OR -wo for writeOverlap, not both. *****";
return false;
} else if (getWriteB()) {
_errorMsg = "\n***** ERROR: request either -wb for writeB OR -wo for writeOverlap, not both. *****";
return false;
} else if (getWriteCount()) {
_errorMsg = "\n***** ERROR: request either -c for writeCount OR -wo for writeOverlap, not both. *****";
return false;
} else if (getAnyHit()) {
_errorMsg = "\n***** ERROR: request either -u for anyHit OR -wo for writeOverlap, not both. *****";
return false;
} else if (getQueryFileType() == FileRecordTypeChecker::BAM_FILE_TYPE && !getExplicitBedOutput()) {
_errorMsg = "\n***** ERROR: writeAllOverlap option is not valid with BAM query input, unless bed output is specified with -bed option. *****";
return false;
}
}
if (getWriteB() || getLeftJoin()) {
if (getQueryFileType() == FileRecordTypeChecker::BAM_FILE_TYPE && !getExplicitBedOutput()) {
cerr << endl << "*****" << endl << "*****WARNING: -wb and -loj are ignored with bam input, unless bed output is specified with -bed option." << endl << "*****" << endl;
}
}
if (getSameStrand() && getDiffStrand()) {
_errorMsg = "\n***** ERROR: request -s for sameStrand, or -S for diffStrand, not both. *****";
return false;
}
if (getQueryFileType() == FileRecordTypeChecker::BAM_FILE_TYPE && getPrintHeader()) {
cerr << endl << "*****" << endl << "*****WARNING: -header option is not valid for BAM input." << endl << "*****" << endl;
setPrintHeader(false);
}
if (getAnyHit() || getNoHit() || getWriteCount()) {
setPrintable(false);
}
if (_files.size() < 2 ) {
return false;
}
return true;
}
