ContextMap::ContextMap()
{
// map requires sorted input
setSortedInput(true);
setLeftJoin(true);
setColumnOpsMethods(true);
}
ContextMerge::ContextMerge()
{
setSortedInput(true);
setUseMergedIntervals(true);
setColumnOpsMethods(true);
setExplicitBedOutput(true);
//merge has no default columnOps the way map does, so we'll need to clear those.
_keyListOps->setColumns("");
_keyListOps->setOperations("");
}
ContextGroupBy::ContextGroupBy()
: _printFullCols(false),
_ignoreCase(false)
{
setSortedInput(true);
_noEnforceCoordSort = true;
setColumnOpsMethods(true);
setExplicitBedOutput(true);
//For columnOps, groupBy has default operation sum but no default column,
///so we have to clear that.
//
_keyListOps->setColumns("");
}
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;
}
