bool ContextBase::strandedToolSupported() {
//Test that all files have strands. Should be called if any tool
// invoked with sameStrand / diffStrand option.
for (int i=0; i < getNumInputFiles(); i++) {
// make sure file has strand.
if (!getFile(i)->recordsHaveStrand()) {
_errorMsg = "\n***** ERROR: stranded ";
_errorMsg += _origProgramName;
_errorMsg += " requested, but input file ";
_errorMsg += getInputFileName(i);
_errorMsg += " does not have strands. *****";
return false;
}
//make sure file is not VCF.
if (getFile(i)->getFileType() == FileRecordTypeChecker::VCF_FILE_TYPE) {
_errorMsg = "\n***** ERROR: stranded ";
_errorMsg += _origProgramName;
_errorMsg += " not supported for VCF file ";
_errorMsg += getInputFileName(i);
_errorMsg += ". *****";
return false;
}
}
return true;
}
bool ContextIntersect::handle_abam()
{
if (_argc <= _i+1) {
_errorMsg = "\n***** ERROR: -abam option given, but no query BAM file specified. *****";
return false;
}
addInputFile(_argv[_i+1]);
_queryFileIdx = getNumInputFiles() -1;
markUsed(_i - _skipFirstArgs);
_i++;
markUsed(_i - _skipFirstArgs);
return true;
}
bool ContextGroupBy::isValidState()
{
// The user was required to have entered one or more columns
if (_keyListOps->getColumns().empty()) {
_errorMsg = "***** ERROR: -opCols parameter requires a value.";
return false;
}
//default to stdin
if (getNumInputFiles() == 0) {
addInputFile("-");
}
//default grouping is cols 1,2,3
if (_groupStr.empty()) _groupStr = "1,2,3";
return ContextBase::isValidState();
}
bool ContextIntersect::handle_b()
{
if (_argc <= _i+1) {
_errorMsg = "\n***** ERROR: -b option given, but no database file specified. *****";
return false;
}
do {
addInputFile(_argv[_i+1]);
int fileId = getNumInputFiles() -1;
_dbFileIdxs.push_back(fileId);
_fileIdsToDbIdxs[fileId] = _dbFileIdxs.size() -1;
markUsed(_i - _skipFirstArgs);
_i++;
markUsed(_i - _skipFirstArgs);
} while (_argc > _i+1 && _argv[_i+1][0] != '-');
return true;
}
bool ContextFisher::isValidState()
{
if (!ContextIntersect::isValidState()) {
return false;
}
// Tests for stranded merge
//
if (_desiredStrand != FileRecordMergeMgr::ANY_STRAND) { // requested stranded merge
for (int i=0; i < getNumInputFiles(); i++) {
// make sure file has strand.
if (!getFile(i)->recordsHaveStrand()) {
_errorMsg = "\n***** ERROR: stranded merge requested, but input file ";
_errorMsg += getInputFileName(i);
_errorMsg += " does not have strands. *****";
return false;
}
//make sure file is not VCF.
if (getFile(1)->getFileType() == FileRecordTypeChecker::VCF_FILE_TYPE) {
_errorMsg = "\n***** ERROR: stranded merge not supported for VCF file ";
_errorMsg += getInputFileName(i);
_errorMsg += ". *****";
return false;
}
}
}
if (_genomeFile == NULL){
_errorMsg = "\nERROR*****: specify -g genome file*****\n";
return false;
}
//column operations not allowed with BAM input
if (hasColumnOpsMethods() &&
getFile(0)->getFileType() == FileRecordTypeChecker::BAM_FILE_TYPE) {
_errorMsg = "\n***** ERROR: stranded merge not supported for VCF files. *****";
return false;
}
return true;
}
bool ContextMerge::isValidState()
{
// Special: The merge program does not have default
//column operations, so if none were entered, disable column ops.
if (_keyListOps->getColumns().empty() && _keyListOps->getOperations().empty()) {
setColumnOpsMethods(false);
delete _keyListOps;
_keyListOps = NULL;
}
//default to stdin
if (getNumInputFiles() == 0) {
addInputFile("-");
}
if (!ContextBase::isValidState()) {
return false;
}
//
// Tests for stranded merge
//
if (_desiredStrand != FileRecordMergeMgr::ANY_STRAND) { // requested stranded merge
// make sure file has strand.
if (!getFile(0)->recordsHaveStrand()) {
_errorMsg = "\n***** ERROR: stranded merge requested, but input file records do not have strand. *****";
return false;
}
//make sure file is not VCF.
if (getFile(0)->getFileType() == FileRecordTypeChecker::VCF_FILE_TYPE) {
_errorMsg = "\n***** ERROR: stranded merge not supported for VCF files. *****";
return false;
}
}
return true;
}
